api_and_parsing.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "708ebf81",
   "metadata": {},
   "source": [
    "# Proteins API\n",
    "\n",
    "Documentation: https://www.ebi.ac.uk/proteins/api/doc/\n",
    "\n",
    "The API domain is **https://www.ebi.ac.uk/proteins/api**. It offers many end-points, we will see here the **proteins**, **taxonomy** and **uniparc** end-points. \n",
    "\n",
    "The output format have to be specified in the request header under the **Accept** field. \n",
    "Available options for the proteins end-point are: \n",
    "\n",
    "- text/x-flatfile\n",
    "- text/x-fasta\n",
    "- application/json\n",
    "- application/xml\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "fecfcd6a",
   "metadata": {},
   "outputs": [],
   "source": [
    "# Documentaiton of the requests module \n",
    "# https://docs.python-requests.org/en/latest/\n",
    "\n",
    "import requests"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "e5616e1b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      ">sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RPO21 PE=1 SV=2\n",
      "MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS\n",
      "IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE\n",
      "LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK\n",
      "LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP\n",
      "VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV\n",
      "ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE\n",
      "LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR\n",
      "AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA\n",
      "DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF\n",
      "IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP\n",
      "KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN\n",
      "GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR\n",
      "FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV\n",
      "DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR\n",
      "LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD\n",
      "LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI\n",
      "RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC\n",
      "LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT\n",
      "LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH\n",
      "TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA\n",
      "AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML\n",
      "KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP\n",
      "GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG\n",
      "LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA\n",
      "FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS\n",
      "NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS\n",
      "PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS\n",
      "PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP\n",
      "SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR\n",
      "\n"
     ]
    }
   ],
   "source": [
    "URL = \"https://www.ebi.ac.uk/proteins/api\"\n",
    "URL_proteins = \"{}/proteins\".format(URL)\n",
    "\n",
    "# Retrieve one protein\n",
    "r = requests.get(\"{}/P04050\".format(URL_proteins), headers={'Accept': 'text/x-fasta'})\n",
    "print(r.status_code)\n",
    "print(r.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "7e793a56",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      ">sp|P04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=RPO21 PE=1 SV=2\n",
      "MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGS\n",
      "IDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNE\n",
      "LMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLK\n",
      "LVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLP\n",
      "VPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHV\n",
      "ATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLE\n",
      "LDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKR\n",
      "AGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNA\n",
      "DFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTF\n",
      "IELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSP\n",
      "KDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHN\n",
      "GFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVR\n",
      "FLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFV\n",
      "DRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR\n",
      "LVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVD\n",
      "LLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNI\n",
      "RRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCC\n",
      "LLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMT\n",
      "LNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEH\n",
      "TTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRA\n",
      "AMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHML\n",
      "KKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP\n",
      "GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGG\n",
      "LTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGA\n",
      "FDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGS\n",
      "NDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTS\n",
      "PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS\n",
      "PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP\n",
      "SYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR\n",
      ">sp|P04637|P53_HUMAN Cellular tumor antigen p53 OS=Homo sapiens OX=9606 GN=TP53 PE=1 SV=4\n",
      "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP\n",
      "DEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAK\n",
      "SVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHE\n",
      "RCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNS\n",
      "SCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELP\n",
      "PGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPG\n",
      "GSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Retrieve more proteins (query parameters)\n",
    "r = requests.get(URL_proteins, params={'accession': 'P04050,P04637'}, headers={'Accept': 'text/x-fasta'})\n",
    "print(r.status_code)\n",
    "print(r.text)"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "cd1adcc4",
   "metadata": {},
   "source": [
    "### Taxonomy\n",
    "\n",
    "Sub end-points: \n",
    "- id\n",
    "- lineage\n",
    "\n",
    "Available formats:\n",
    "- application/json\n",
    "- application/xml"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "cc0b753e",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "{'taxonomyId': 9606, 'mnemonic': 'HUMAN', 'scientificName': 'Homo sapiens', 'commonName': 'Human', 'rank': 'species', 'superregnum': 'E', 'hidden': True, 'parentLink': 'https://www.ebi.ac.uk/proteins/api/taxonomy/id/9605', 'childrenLinks': ['https://www.ebi.ac.uk/proteins/api/taxonomy/id/741158', 'https://www.ebi.ac.uk/proteins/api/taxonomy/id/63221'], 'siblingsLinks': ['https://www.ebi.ac.uk/proteins/api/taxonomy/id/2665952', 'https://www.ebi.ac.uk/proteins/api/taxonomy/id/1425170']}\n"
     ]
    }
   ],
   "source": [
    "\n",
    "URL_taxonomy = \"{}/taxonomy\".format(URL)\n",
    "\n",
    "# Find single node\n",
    "r = requests.get(\"{}/id/9606\".format(URL_taxonomy), headers={'Accept': 'application/json'})\n",
    "print(r.status_code)\n",
    "print(r.json())\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "feb948da",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "{'taxonomyId': 9606, 'scientificName': 'Homo sapiens', 'rank': 'species', 'hidden': True}\n",
      "{'taxonomyId': 9605, 'scientificName': 'Homo', 'rank': 'genus', 'hidden': False}\n",
      "{'taxonomyId': 207598, 'scientificName': 'Homininae', 'rank': 'subfamily', 'hidden': True}\n",
      "{'taxonomyId': 9604, 'scientificName': 'Hominidae', 'rank': 'family', 'hidden': False}\n",
      "{'taxonomyId': 314295, 'scientificName': 'Hominoidea', 'rank': 'superfamily', 'hidden': True}\n",
      "{'taxonomyId': 9526, 'scientificName': 'Catarrhini', 'rank': 'parvorder', 'hidden': False}\n",
      "{'taxonomyId': 314293, 'scientificName': 'Simiiformes', 'rank': 'infraorder', 'hidden': True}\n",
      "{'taxonomyId': 376913, 'scientificName': 'Haplorrhini', 'rank': 'suborder', 'hidden': False}\n",
      "{'taxonomyId': 9443, 'scientificName': 'Primates', 'rank': 'order', 'hidden': False}\n",
      "{'taxonomyId': 314146, 'scientificName': 'Euarchontoglires', 'rank': 'superorder', 'hidden': False}\n",
      "{'taxonomyId': 1437010, 'scientificName': 'Boreoeutheria', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 9347, 'scientificName': 'Eutheria', 'rank': 'no rank', 'hidden': False}\n",
      "{'taxonomyId': 32525, 'scientificName': 'Theria', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 40674, 'scientificName': 'Mammalia', 'rank': 'class', 'hidden': False}\n",
      "{'taxonomyId': 32524, 'scientificName': 'Amniota', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 32523, 'scientificName': 'Tetrapoda', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 1338369, 'scientificName': 'Dipnotetrapodomorpha', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 8287, 'scientificName': 'Sarcopterygii', 'rank': 'superclass', 'hidden': True}\n",
      "{'taxonomyId': 117571, 'scientificName': 'Euteleostomi', 'rank': 'no rank', 'hidden': False}\n",
      "{'taxonomyId': 117570, 'scientificName': 'Teleostomi', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 7776, 'scientificName': 'Gnathostomata', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 7742, 'scientificName': 'Vertebrata', 'rank': 'no rank', 'hidden': False}\n",
      "{'taxonomyId': 89593, 'scientificName': 'Craniata', 'rank': 'subphylum', 'hidden': False}\n",
      "{'taxonomyId': 7711, 'scientificName': 'Chordata', 'rank': 'phylum', 'hidden': False}\n",
      "{'taxonomyId': 33511, 'scientificName': 'Deuterostomia', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 33213, 'scientificName': 'Bilateria', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 6072, 'scientificName': 'Eumetazoa', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 33208, 'scientificName': 'Metazoa', 'rank': 'kingdom', 'hidden': False}\n",
      "{'taxonomyId': 33154, 'scientificName': 'Opisthokonta', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 2759, 'scientificName': 'Eukaryota', 'rank': 'superkingdom', 'hidden': False}\n",
      "{'taxonomyId': 131567, 'scientificName': 'cellular organisms', 'rank': 'no rank', 'hidden': True}\n",
      "{'taxonomyId': 1, 'scientificName': 'root', 'rank': 'no rank', 'hidden': True}\n"
     ]
    }
   ],
   "source": [
    "# Full lineage\n",
    "# Note some nodes are annotated as hidden. Hidden nodes are not included in the UniProt standard lineage\n",
    "r = requests.get(\"{}/lineage/9606\".format(URL_taxonomy), headers={'Accept': 'application/json'})\n",
    "print(r.status_code)\n",
    "for node in r.json()['taxonomies']:\n",
    "    print(node)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "20ca8593",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "rank                scientificName           commonName          \n",
      "species             Homo sapiens             Human               \n",
      "genus               Homo                     None                \n",
      "subfamily           Homininae                None                \n",
      "family              Hominidae                great apes          \n",
      "superfamily         Hominoidea               apes                \n",
      "parvorder           Catarrhini               None                \n",
      "infraorder          Simiiformes              None                \n",
      "suborder            Haplorrhini              None                \n",
      "order               Primates                 None                \n",
      "superorder          Euarchontoglires         None                \n",
      "no rank             Boreoeutheria            None                \n",
      "no rank             Eutheria                 placentals          \n",
      "no rank             Theria                   None                \n",
      "class               Mammalia                 mammals             \n",
      "no rank             Amniota                  amniotes            \n",
      "no rank             Tetrapoda                tetrapods           \n",
      "no rank             Dipnotetrapodomorpha     None                \n",
      "superclass          Sarcopterygii            None                \n",
      "no rank             Euteleostomi             bony vertebrates    \n",
      "no rank             Teleostomi               None                \n",
      "no rank             Gnathostomata            jawed vertebrates   \n",
      "no rank             Vertebrata               vertebrates         \n",
      "subphylum           Craniata                 None                \n",
      "phylum              Chordata                 chordates           \n",
      "no rank             Deuterostomia            None                \n",
      "no rank             Bilateria                None                \n",
      "no rank             Eumetazoa                None                \n",
      "kingdom             Metazoa                  metazoans           \n",
      "no rank             Opisthokonta             None                \n",
      "superkingdom        Eukaryota                eucaryotes          \n",
      "no rank             cellular organisms       None                \n",
      "no rank             root                     None                \n"
     ]
    }
   ],
   "source": [
    "# Find full Homo sapiens lineage (taxon ID: 9606) using a recursive function\n",
    "\n",
    "def build_lineage(taxon_id, url, lineage=[], include_hidden=False):\n",
    "    req = \"{}/{}\".format(url, taxon_id)\n",
    "    r = requests.get(req, headers={'Accept': 'application/json'})\n",
    "    if r.status_code == 200:\n",
    "        node = r.json()\n",
    "        if include_hidden or not node.get(\"hidden\"):\n",
    "            lineage.append(node)\n",
    "        if node.get(\"parentLink\"):\n",
    "            parent_id = node[\"parentLink\"].split(\"/\")[-1]\n",
    "            return build_lineage(parent_id, url, lineage, include_hidden)\n",
    "        else:\n",
    "            return lineage\n",
    "    else:\n",
    "        return r\n",
    "\n",
    "\n",
    "path = build_lineage(\"9606\", \"{}/taxonomy/id\".format(URL), include_hidden=True)\n",
    "fields = ['rank', 'scientificName', 'commonName']\n",
    "print(\"{:<20}{:<25}{:<20}\".format(*fields))\n",
    "for node in path:\n",
    "    print(\"{:<20}{:<25}{:<20}\".format(*[str(node.get(field)) for field in fields]))"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "70693f10",
   "metadata": {},
   "source": [
    "# Website API\n",
    "\n",
    "Documentation: https://www.uniprot.org/help/api\n",
    "\n",
    "The API domain is **https://www.uniprot.org**. It offers many end-points, we will see here the **uniprot** **uploadlists** end-points. \n",
    "\n",
    "The **uniprot** end-point allows to search (**query**) and download UniProt entries in various formats. The format can be specified either in the URL (as extention) or in the request headers (as in the \"Proteins API\" above).\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "94d73df4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "ID   RPB1_YEAST              Reviewed;        1733 AA.\n",
      "AC   P04050; D6VRK8; Q12364; Q92315;\n",
      "DT   01-NOV-1986, integrated into UniProtKB/Swiss-Prot.\n",
      "DT   01-NOV-1997, sequence version 2.\n",
      "DT   29-SEP-2021, entry version 233.\n",
      "DE   RecName: Full=DNA-directed RNA polymerase II subunit RPB1;\n",
      "DE            Short=RNA polymerase II subunit 1;\n",
      "DE            Short=RNA polymerase II subunit B1;\n",
      "DE            EC=2.7.7.6;\n",
      "DE   AltName: Full=DNA-directed RNA polymerase III largest subunit;\n",
      "DE   AltName: Full=RNA polymerase II subunit B220;\n",
      "GN   Name=RPO21; Synonyms=RPB1, RPB220, SUA8; OrderedLocusNames=YDL140C;\n",
      "GN   ORFNames=D2150;\n",
      "OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).\n",
      "OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;\n",
      "OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.\n",
      "OX   NCBI_TaxID=559292;\n",
      "RN   [1]\n",
      "RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].\n",
      "RC   STRAIN=ATCC 204626 / S288c / A364A;\n",
      "RX   PubMed=3896517; DOI=10.1016/0092-8674(85)90117-5;\n",
      "RA   Allison L.A., Moyle M., Shales M., Ingles C.J.;\n",
      "RT   \"Extensive homology among the largest subunits of eukaryotic and\n",
      "RT   prokaryotic RNA polymerases.\";\n",
      "RL   Cell 42:599-610(1985).\n",
      "RN   [2]\n",
      "RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].\n",
      "RC   STRAIN=ATCC 96604 / S288c / FY1679;\n",
      "RX   PubMed=8972577;\n",
      "RX   DOI=10.1002/(sici)1097-0061(199612)12:15<1549::aid-yea42>3.0.co;2-s;\n",
      "RA   Woelfl S., Haneman V., Saluz H.P.;\n",
      "RT   \"Analysis of a 26,756 bp segment from the left arm of yeast chromosome\n",
      "RT   IV.\";\n",
      "RL   Yeast 12:1549-1554(1996).\n",
      "RN   [3]\n",
      "RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].\n",
      "RC   STRAIN=ATCC 204508 / S288c;\n",
      "RX   PubMed=9169867;\n",
      "RA   Jacq C., Alt-Moerbe J., Andre B., Arnold W., Bahr A., Ballesta J.P.G.,\n",
      "RA   Bargues M., Baron L., Becker A., Biteau N., Bloecker H., Blugeon C.,\n",
      "RA   Boskovic J., Brandt P., Brueckner M., Buitrago M.J., Coster F.,\n",
      "RA   Delaveau T., del Rey F., Dujon B., Eide L.G., Garcia-Cantalejo J.M.,\n",
      "RA   Goffeau A., Gomez-Peris A., Granotier C., Hanemann V., Hankeln T.,\n",
      "RA   Hoheisel J.D., Jaeger W., Jimenez A., Jonniaux J.-L., Kraemer C.,\n",
      "RA   Kuester H., Laamanen P., Legros Y., Louis E.J., Moeller-Rieker S.,\n",
      "RA   Monnet A., Moro M., Mueller-Auer S., Nussbaumer B., Paricio N., Paulin L.,\n",
      "RA   Perea J., Perez-Alonso M., Perez-Ortin J.E., Pohl T.M., Prydz H.,\n",
      "RA   Purnelle B., Rasmussen S.W., Remacha M.A., Revuelta J.L., Rieger M.,\n",
      "RA   Salom D., Saluz H.P., Saiz J.E., Saren A.-M., Schaefer M., Scharfe M.,\n",
      "RA   Schmidt E.R., Schneider C., Scholler P., Schwarz S., Soler-Mira A.,\n",
      "RA   Urrestarazu L.A., Verhasselt P., Vissers S., Voet M., Volckaert G.,\n",
      "RA   Wagner G., Wambutt R., Wedler E., Wedler H., Woelfl S., Harris D.E.,\n",
      "RA   Bowman S., Brown D., Churcher C.M., Connor R., Dedman K., Gentles S.,\n",
      "RA   Hamlin N., Hunt S., Jones L., McDonald S., Murphy L.D., Niblett D.,\n",
      "RA   Odell C., Oliver K., Rajandream M.A., Richards C., Shore L., Walsh S.V.,\n",
      "RA   Barrell B.G., Dietrich F.S., Mulligan J.T., Allen E., Araujo R., Aviles E.,\n",
      "RA   Berno A., Carpenter J., Chen E., Cherry J.M., Chung E., Duncan M.,\n",
      "RA   Hunicke-Smith S., Hyman R.W., Komp C., Lashkari D., Lew H., Lin D.,\n",
      "RA   Mosedale D., Nakahara K., Namath A., Oefner P., Oh C., Petel F.X.,\n",
      "RA   Roberts D., Schramm S., Schroeder M., Shogren T., Shroff N., Winant A.,\n",
      "RA   Yelton M.A., Botstein D., Davis R.W., Johnston M., Andrews S., Brinkman R.,\n",
      "RA   Cooper J., Ding H., Du Z., Favello A., Fulton L., Gattung S., Greco T.,\n",
      "RA   Hallsworth K., Hawkins J., Hillier L.W., Jier M., Johnson D., Johnston L.,\n",
      "RA   Kirsten J., Kucaba T., Langston Y., Latreille P., Le T., Mardis E.,\n",
      "RA   Menezes S., Miller N., Nhan M., Pauley A., Peluso D., Rifkin L., Riles L.,\n",
      "RA   Taich A., Trevaskis E., Vignati D., Wilcox L., Wohldman P., Vaudin M.,\n",
      "RA   Wilson R., Waterston R., Albermann K., Hani J., Heumann K., Kleine K.,\n",
      "RA   Mewes H.-W., Zollner A., Zaccaria P.;\n",
      "RT   \"The nucleotide sequence of Saccharomyces cerevisiae chromosome IV.\";\n",
      "RL   Nature 387:75-78(1997).\n",
      "RN   [4]\n",
      "RP   GENOME REANNOTATION.\n",
      "RC   STRAIN=ATCC 204508 / S288c;\n",
      "RX   PubMed=24374639; DOI=10.1534/g3.113.008995;\n",
      "RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,\n",
      "RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,\n",
      "RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;\n",
      "RT   \"The reference genome sequence of Saccharomyces cerevisiae: Then and now.\";\n",
      "RL   G3 (Bethesda) 4:389-398(2014).\n",
      "RN   [5]\n",
      "RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1669-1733.\n",
      "RC   STRAIN=ATCC 204508 / S288c;\n",
      "RX   PubMed=7649444; DOI=10.1111/j.1574-6968.1995.tb07724.x;\n",
      "RA   Cronan J.E. Jr., Wallace J.C.;\n",
      "RT   \"The gene encoding the biotin-apoprotein ligase of Saccharomyces\n",
      "RT   cerevisiae.\";\n",
      "RL   FEMS Microbiol. Lett. 130:221-230(1995).\n",
      "RN   [6]\n",
      "RP   MUTAGENESIS OF THE CTD.\n",
      "RX   PubMed=7498765;\n",
      "RA   West M.L., Corden J.L.;\n",
      "RT   \"Construction and analysis of yeast RNA polymerase II CTD deletion and\n",
      "RT   substitution mutations.\";\n",
      "RL   Genetics 140:1223-1233(1995).\n",
      "RN   [7]\n",
      "RP   PHOSPHORYLATION BY THE TFIIK COMPLEX AND THE SRB8-11 COMPLEX.\n",
      "RX   PubMed=9702190; DOI=10.1016/s1097-2765(00)80112-4;\n",
      "RA   Hengartner C.J., Myer V.E., Liao S.-M., Wilson C.J., Koh S.S., Young R.A.;\n",
      "RT   \"Temporal regulation of RNA polymerase II by Srb10 and Kin28 cyclin-\n",
      "RT   dependent kinases.\";\n",
      "RL   Mol. Cell 2:43-53(1998).\n",
      "RN   [8]\n",
      "RP   INTERACTION WITH ESS1.\n",
      "RX   PubMed=10531363; DOI=10.1074/jbc.274.44.31583;\n",
      "RA   Morris D.P., Phatnani H.P., Greenleaf A.L.;\n",
      "RT   \"Phospho-carboxyl-terminal domain binding and the role of a prolyl\n",
      "RT   isomerase in pre-mRNA 3'-End formation.\";\n",
      "RL   J. Biol. Chem. 274:31583-31587(1999).\n",
      "RN   [9]\n",
      "RP   DEPHOSPHORYLATION BY FCP1.\n",
      "RX   PubMed=10445027; DOI=10.1016/s1097-2765(00)80187-2;\n",
      "RA   Kobor M.S., Archambault J., Lester W., Holstege F.C.P., Gileadi O.,\n",
      "RA   Jansma D.B., Jennings E.G., Kouyoumdjian F., Davidson A.R., Young R.A.,\n",
      "RA   Greenblatt J.;\n",
      "RT   \"An unusual eukaryotic protein phosphatase required for transcription by\n",
      "RT   RNA polymerase II and CTD dephosphorylation in S. cerevisiae.\";\n",
      "RL   Mol. Cell 4:55-62(1999).\n",
      "RN   [10]\n",
      "RP   PHOSPHORYLATION BY THE BUR KINASE COMPLEX.\n",
      "RX   PubMed=11390638; DOI=10.1128/mcb.21.13.4089-4096.2001;\n",
      "RA   Murray S., Udupa R., Yao S., Hartzog G., Prelich G.;\n",
      "RT   \"Phosphorylation of the RNA polymerase II carboxy-terminal domain by the\n",
      "RT   Bur1 cyclin-dependent kinase.\";\n",
      "RL   Mol. Cell. Biol. 21:4089-4096(2001).\n",
      "RN   [11]\n",
      "RP   INTERACTION WITH ASK10.\n",
      "RX   PubMed=14555478; DOI=10.1128/ec.2.5.962-970.2003;\n",
      "RA   Cohen T.J., Lee K., Rutkowski L.H., Strich R.;\n",
      "RT   \"Ask10p mediates the oxidative stress-induced destruction of the\n",
      "RT   Saccharomyces cerevisiae C-type cyclin Ume3p/Srb11p.\";\n",
      "RL   Eukaryot. Cell 2:962-970(2003).\n",
      "RN   [12]\n",
      "RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-695, AND IDENTIFICATION BY\n",
      "RP   MASS SPECTROMETRY.\n",
      "RX   PubMed=14557538; DOI=10.1073/pnas.2135500100;\n",
      "RA   Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.;\n",
      "RT   \"A subset of membrane-associated proteins is ubiquitinated in response to\n",
      "RT   mutations in the endoplasmic reticulum degradation machinery.\";\n",
      "RL   Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003).\n",
      "RN   [13]\n",
      "RP   PHOSPHORYLATION BY CTD KINASE.\n",
      "RX   PubMed=15047695; DOI=10.1074/jbc.m402218200;\n",
      "RA   Jones J.C., Phatnani H.P., Haystead T.A., MacDonald J.A., Alam S.M.,\n",
      "RA   Greenleaf A.L.;\n",
      "RT   \"C-terminal repeat domain kinase I phosphorylates Ser2 and Ser5 of RNA\n",
      "RT   polymerase II C-terminal domain repeats.\";\n",
      "RL   J. Biol. Chem. 279:24957-24964(2004).\n",
      "RN   [14]\n",
      "RP   INTERACTION WITH RTT103.\n",
      "RX   PubMed=15565157; DOI=10.1038/nature03041;\n",
      "RA   Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F.,\n",
      "RA   Buratowski S.;\n",
      "RT   \"The yeast Rat1 exonuclease promotes transcription termination by RNA\n",
      "RT   polymerase II.\";\n",
      "RL   Nature 432:517-522(2004).\n",
      "RN   [15]\n",
      "RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].\n",
      "RC   STRAIN=ADR376;\n",
      "RX   PubMed=17330950; DOI=10.1021/pr060559j;\n",
      "RA   Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J.,\n",
      "RA   Elias J.E., Gygi S.P.;\n",
      "RT   \"Large-scale phosphorylation analysis of alpha-factor-arrested\n",
      "RT   Saccharomyces cerevisiae.\";\n",
      "RL   J. Proteome Res. 6:1190-1197(2007).\n",
      "RN   [16]\n",
      "RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-1471, AND IDENTIFICATION BY\n",
      "RP   MASS SPECTROMETRY [LARGE SCALE ANALYSIS].\n",
      "RX   PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;\n",
      "RA   Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;\n",
      "RT   \"A multidimensional chromatography technology for in-depth phosphoproteome\n",
      "RT   analysis.\";\n",
      "RL   Mol. Cell. Proteomics 7:1389-1396(2008).\n",
      "RN   [17]\n",
      "RP   INTERACTION WITH SHE2.\n",
      "RX   PubMed=20713510; DOI=10.1101/gad.1937510;\n",
      "RA   Shen Z., St-Denis A., Chartrand P.;\n",
      "RT   \"Cotranscriptional recruitment of She2p by RNA pol II elongation factor\n",
      "RT   Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud.\";\n",
      "RL   Genes Dev. 24:1914-1926(2010).\n",
      "RN   [18]\n",
      "RP   UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-695; LYS-1246 AND LYS-1350,\n",
      "RP   AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].\n",
      "RX   PubMed=22106047; DOI=10.1002/pmic.201100166;\n",
      "RA   Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.;\n",
      "RT   \"Sites of ubiquitin attachment in Saccharomyces cerevisiae.\";\n",
      "RL   Proteomics 12:236-240(2012).\n",
      "RN   [19]\n",
      "RP   ELECTRON MICROSCOPY OF THE RNA POL II/TFIIF COMPLEX.\n",
      "RX   PubMed=14580350; DOI=10.1016/s1097-2765(03)00387-3;\n",
      "RA   Chung W.H., Craighead J.L., Chang W.H., Ezeokonkwo C., Bareket-Samish A.,\n",
      "RA   Kornberg R.D., Asturias F.J.;\n",
      "RT   \"RNA polymerase II/TFIIF structure and conserved organization of the\n",
      "RT   initiation complex.\";\n",
      "RL   Mol. Cell 12:1003-1013(2003).\n",
      "RN   [20]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.\n",
      "RX   PubMed=11313498; DOI=10.1126/science.1059493;\n",
      "RA   Cramer P., Bushnell D.A., Kornberg R.D.;\n",
      "RT   \"Structural basis of transcription: RNA polymerase II at 2.8 A\n",
      "RT   resolution.\";\n",
      "RL   Science 292:1863-1876(2001).\n",
      "RN   [21]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (3.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.\n",
      "RX   PubMed=11313499; DOI=10.1126/science.1059495;\n",
      "RA   Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D.;\n",
      "RT   \"Structural basis of transcription: an RNA polymerase II elongation complex\n",
      "RT   at 3.3 A resolution.\";\n",
      "RL   Science 292:1876-1882(2001).\n",
      "RN   [22]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF THE RNA POL II CORE COMPLEX IN\n",
      "RP   COMPLEX WITH ALPHA-AMANITIN.\n",
      "RX   PubMed=11805306; DOI=10.1073/pnas.251664698;\n",
      "RA   Bushnell D.A., Cramer P., Kornberg R.D.;\n",
      "RT   \"Structural basis of transcription: alpha-amanitin-RNA polymerase II\n",
      "RT   cocrystal at 2.8 A resolution.\";\n",
      "RL   Proc. Natl. Acad. Sci. U.S.A. 99:1218-1222(2002).\n",
      "RN   [23]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX\n",
      "RP   WITH DST1.\n",
      "RX   PubMed=12914699; DOI=10.1016/s0092-8674(03)00598-1;\n",
      "RA   Kettenberger H., Armache K.J., Cramer P.;\n",
      "RT   \"Architecture of the RNA polymerase II-TFIIS complex and implications for\n",
      "RT   mRNA cleavage.\";\n",
      "RL   Cell 114:347-357(2003).\n",
      "RN   [24]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (4.2 ANGSTROMS) OF THE RNA POL II COMPLEX.\n",
      "RX   PubMed=12746495; DOI=10.1073/pnas.1030608100;\n",
      "RA   Armache K.J., Kettenberger H., Cramer P.;\n",
      "RT   \"Architecture of initiation-competent 12-subunit RNA polymerase II.\";\n",
      "RL   Proc. Natl. Acad. Sci. U.S.A. 100:6964-6968(2003).\n",
      "RN   [25]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (4.1 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.\n",
      "RX   PubMed=12746498; DOI=10.1073/pnas.1130601100;\n",
      "RA   Bushnell D.A., Kornberg R.D.;\n",
      "RT   \"Complete, 12-subunit RNA polymerase II at 4.1-A resolution: implications\n",
      "RT   for the initiation of transcription.\";\n",
      "RL   Proc. Natl. Acad. Sci. U.S.A. 100:6969-6973(2003).\n",
      "RN   [26]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.\n",
      "RX   PubMed=15537538; DOI=10.1016/j.cell.2004.10.016;\n",
      "RA   Westover K.D., Bushnell D.A., Kornberg R.D.;\n",
      "RT   \"Structural basis of transcription: nucleotide selection by rotation in the\n",
      "RT   RNA polymerase II active center.\";\n",
      "RL   Cell 119:481-489(2004).\n",
      "RN   [27]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS).\n",
      "RX   PubMed=15610738; DOI=10.1016/j.molcel.2004.11.040;\n",
      "RA   Kettenberger H., Armache K.J., Cramer P.;\n",
      "RT   \"Complete RNA polymerase II elongation complex structure and its\n",
      "RT   interactions with NTP and TFIIS.\";\n",
      "RL   Mol. Cell 16:955-965(2004).\n",
      "RN   [28]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (4.5 ANGSTROMS) OF THE RNA POL II CORE COMPLEX.\n",
      "RX   PubMed=14963322; DOI=10.1126/science.1090838;\n",
      "RA   Bushnell D.A., Westover K.D., Davis R.E., Kornberg R.D.;\n",
      "RT   \"Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at\n",
      "RT   4.5 Angstroms.\";\n",
      "RL   Science 303:983-988(2004).\n",
      "RN   [29]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX.\n",
      "RX   PubMed=15591044; DOI=10.1074/jbc.m413038200;\n",
      "RA   Armache K.J., Mitterweger S., Meinhart A., Cramer P.;\n",
      "RT   \"Structures of complete RNA polymerase II and its subcomplex, Rpb4/7.\";\n",
      "RL   J. Biol. Chem. 280:7131-7134(2005).\n",
      "RN   [30]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (3.8 ANGSTROMS) OF THE RNA POL II COMPLEX IN COMPLEX\n",
      "RP   WITH INHIBITING NON-CODING RNA.\n",
      "RX   PubMed=16341226; DOI=10.1038/nsmb1032;\n",
      "RA   Kettenberger H., Eisenfuhr A., Brueckner F., Theis M., Famulok M.,\n",
      "RA   Cramer P.;\n",
      "RT   \"Structure of an RNA polymerase II-RNA inhibitor complex elucidates\n",
      "RT   transcription regulation by noncoding RNAs.\";\n",
      "RL   Nat. Struct. Mol. Biol. 13:44-48(2006).\n",
      "RN   [31]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (4.15 ANGSTROMS) OF THE RNA POL II COMPLEX.\n",
      "RX   PubMed=16765890; DOI=10.1016/j.str.2006.04.003;\n",
      "RA   Meyer P.A., Ye P., Zhang M., Suh M.H., Fu J.;\n",
      "RT   \"Phasing RNA polymerase II using intrinsically bound Zn atoms: an updated\n",
      "RT   structural model.\";\n",
      "RL   Structure 14:973-982(2006).\n",
      "RN   [32]\n",
      "RP   X-RAY CRYSTALLOGRAPHY (3.40 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND ZINC.\n",
      "RX   PubMed=23151482; DOI=10.1038/nature11715;\n",
      "RA   Sainsbury S., Niesser J., Cramer P.;\n",
      "RT   \"Structure and function of the initially transcribing RNA polymerase II-\n",
      "RT   TFIIB complex.\";\n",
      "RL   Nature 493:437-440(2013).\n",
      "RN   [33]\n",
      "RP   STRUCTURE BY ELECTRON MICROSCOPY (6.60 ANGSTROMS) IN COMPLEX WITH MAGNESIUM\n",
      "RP   AND ZINC.\n",
      "RX   PubMed=25652824; DOI=10.1038/nature14229;\n",
      "RA   Plaschka C., Lariviere L., Wenzeck L., Seizl M., Hemann M., Tegunov D.,\n",
      "RA   Petrotchenko E.V., Borchers C.H., Baumeister W., Herzog F., Villa E.,\n",
      "RA   Cramer P.;\n",
      "RT   \"Architecture of the RNA polymerase II-Mediator core initiation complex.\";\n",
      "RL   Nature 518:376-380(2015).\n",
      "CC   -!- FUNCTION: DNA-dependent RNA polymerase catalyzes the transcription of\n",
      "CC       DNA into RNA using the four ribonucleoside triphosphates as substrates.\n",
      "CC       Largest and catalytic component of RNA polymerase II which synthesizes\n",
      "CC       mRNA precursors and many functional non-coding RNAs. Forms the\n",
      "CC       polymerase active center together with the second largest subunit. Pol\n",
      "CC       II is the central component of the basal RNA polymerase II\n",
      "CC       transcription machinery. During a transcription cycle, Pol II, general\n",
      "CC       transcription factors and the Mediator complex assemble as the\n",
      "CC       preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA\n",
      "CC       surrounding the transcription start site are melted and the single-\n",
      "CC       stranded DNA template strand of the promoter is positioned deeply\n",
      "CC       within the central active site cleft of Pol II to form the open\n",
      "CC       complex. After synthesis of about 30 bases of RNA, Pol II releases its\n",
      "CC       contacts with the core promoter and the rest of the transcription\n",
      "CC       machinery (promoter clearance) and enters the stage of transcription\n",
      "CC       elongation in which it moves on the template as the transcript\n",
      "CC       elongates. Pol II appears to oscillate between inactive and active\n",
      "CC       conformations at each step of nucleotide addition. Elongation is\n",
      "CC       influenced by the phosphorylation status of the C-terminal domain (CTD)\n",
      "CC       of Pol II largest subunit (RPB1), which serves as a platform for\n",
      "CC       assembly of factors that regulate transcription initiation, elongation,\n",
      "CC       termination and mRNA processing. Pol II is composed of mobile elements\n",
      "CC       that move relative to each other. The core element with the central\n",
      "CC       large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and\n",
      "CC       RPB2 forming the active center. The clamp element (portions of RPB1,\n",
      "CC       RPB2 and RPB3) is connected to the core through a set of flexible\n",
      "CC       switches and moves to open and close the cleft. A bridging helix\n",
      "CC       emanates from RPB1 and crosses the cleft near the catalytic site and is\n",
      "CC       thought to promote translocation of Pol II by acting as a ratchet that\n",
      "CC       moves the RNA-DNA hybrid through the active site by switching from\n",
      "CC       straight to bent conformations at each step of nucleotide addition. In\n",
      "CC       elongating Pol II, the lid loop (RPB1) appears to act as a wedge to\n",
      "CC       drive apart the DNA and RNA strands at the upstream end of the\n",
      "CC       transcription bubble and guide the RNA strand toward the RNA exit\n",
      "CC       groove located near the base of the largely unstructured CTD domain of\n",
      "CC       RPB1. The rudder loop (RPB1) interacts with single-stranded DNA after\n",
      "CC       separation from the RNA strand, likely preventing reassociation with\n",
      "CC       the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed\n",
      "CC       by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and\n",
      "CC       portions of RBP1. The jaws are thought to grab the incoming DNA\n",
      "CC       template, mainly by RPB5 direct contacts to DNA.\n",
      "CC   -!- CATALYTIC ACTIVITY:\n",
      "CC       Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +\n",
      "CC         RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-\n",
      "CC         COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;\n",
      "CC         EC=2.7.7.6;\n",
      "CC   -!- SUBUNIT: Component of the RNA polymerase II (Pol II) complex consisting\n",
      "CC       of 12 subunits. Interacts with ASK10, ESS1, RTT103 and SHE2.\n",
      "CC       {ECO:0000269|PubMed:10531363, ECO:0000269|PubMed:11805306,\n",
      "CC       ECO:0000269|PubMed:12914699, ECO:0000269|PubMed:14555478,\n",
      "CC       ECO:0000269|PubMed:15565157, ECO:0000269|PubMed:16341226,\n",
      "CC       ECO:0000269|PubMed:20713510}.\n",
      "CC   -!- INTERACTION:\n",
      "CC       P04050; Q06697: CDC73; NbExp=17; IntAct=EBI-15760, EBI-29913;\n",
      "CC       P04050; P89105: CTR9; NbExp=4; IntAct=EBI-15760, EBI-5283;\n",
      "CC       P04050; P53617: NRD1; NbExp=2; IntAct=EBI-15760, EBI-12228;\n",
      "CC       P04050; P08518: RPB2; NbExp=4; IntAct=EBI-15760, EBI-15767;\n",
      "CC       P04050; P53064: RTF1; NbExp=7; IntAct=EBI-15760, EBI-16303;\n",
      "CC       P04050; Q00416: SEN1; NbExp=4; IntAct=EBI-15760, EBI-16945;\n",
      "CC       P04050; P27692: SPT5; NbExp=3; IntAct=EBI-15760, EBI-17937;\n",
      "CC   -!- SUBCELLULAR LOCATION: Nucleus.\n",
      "CC   -!- DOMAIN: The C-terminal domain (CTD) serves as a platform for assembly\n",
      "CC       of factors that regulate transcription initiation, elongation,\n",
      "CC       termination and mRNA processing. {ECO:0000305}.\n",
      "CC   -!- PTM: The tandem 7 residues repeats in the C-terminal domain (CTD) can\n",
      "CC       be highly phosphorylated. The phosphorylation activates Pol II.\n",
      "CC       Phosphorylation occurs mainly at residues 'Ser-2' and 'Ser-5' of the\n",
      "CC       heptapeptide repeat. The phosphorylated form of Pol II appears to\n",
      "CC       carry, on average, one phosphate per repeat. The phosphorylation state\n",
      "CC       is believed to result from the balanced action of site-specific CTD\n",
      "CC       kinases and phosphatases, and a 'CTD code' that specifies the position\n",
      "CC       of Pol II within the transcription cycle has been proposed.\n",
      "CC       Phosphorylation at 'Ser-5' occurs in promoter-proximal regions in early\n",
      "CC       elongation. Phosphorylation at 'Ser-2' predominates in regions more\n",
      "CC       distal to the promoter and triggers binding of the 3' RNA processing\n",
      "CC       machinery. CTD kinases include KIN28 (as part of the TFKII complex, a\n",
      "CC       subcomplex of the TFIIH holo complex), SSN3/SRB10 (as part of the SRB8-\n",
      "CC       11 complex, a module of the Mediator complex), CTK1 (as part of CTD\n",
      "CC       kinase), and probably BUR1 (as part of the BUR1-BUR2 kinase complex).\n",
      "CC       Phosphatases include FCP1 and SSU72. {ECO:0000269|PubMed:11390638,\n",
      "CC       ECO:0000269|PubMed:15047695, ECO:0000269|PubMed:9702190}.\n",
      "CC   -!- MISCELLANEOUS: Mutagenesis experiments demonstrate that the minimum\n",
      "CC       viable CTD contains eight consensus Y-S-P-T-S-P-[A-S-N-G] heptapeptide\n",
      "CC       repeats. Identical and simultaneous substitutions in a number of\n",
      "CC       consecutive repeats are lethal: 'Ser-2' -> 'Ala-2' (14 repeats), 'Ser-\n",
      "CC       5' -> 'Ala-5' (15 repeats), '2-Ser-Pro-Thr-Ser-5'-> '2-Ala-Pro-Thr-Ala-\n",
      "CC       5' (10 repeats), 'Ser-2'-> 'Glu-2' (15 repeats), 'Ser-5' -> 'Glu-5' (12\n",
      "CC       repeats), '2-Ser-Pro-3' -> '2-Pro-Ser-3' (15 repeats) and 'Tyr-1' ->\n",
      "CC       'Phe-1' (12 repeats).\n",
      "CC   -!- MISCELLANEOUS: The binding of ribonucleoside triphosphate to the RNA\n",
      "CC       polymerase II transcribing complex probably involves a two-step\n",
      "CC       mechanism. The initial binding seems to occur at the entry (E) site and\n",
      "CC       involves a magnesium ion temporarily coordinated by three conserved\n",
      "CC       aspartate residues of the two largest RNA Pol II subunits. The\n",
      "CC       ribonucleoside triphosphate is transferred by a rotation to the\n",
      "CC       nucleotide addition (A) site for pairing with the template DNA. The\n",
      "CC       catalytic A site involves three conserved aspartate residues of the RNA\n",
      "CC       Pol II largest subunit which permanently coordinate a second magnesium\n",
      "CC       ion.\n",
      "CC   -!- SIMILARITY: Belongs to the RNA polymerase beta' chain family.\n",
      "CC       {ECO:0000305}.\n",
      "CC   ---------------------------------------------------------------------------\n",
      "CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms\n",
      "CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License\n",
      "CC   ---------------------------------------------------------------------------\n",
      "DR   EMBL; X03128; CAA26904.1; -; Genomic_DNA.\n",
      "DR   EMBL; X96876; CAA65619.1; -; Genomic_DNA.\n",
      "DR   EMBL; Z74188; CAA98713.1; -; Genomic_DNA.\n",
      "DR   EMBL; U27182; AAC49058.1; -; Genomic_DNA.\n",
      "DR   EMBL; BK006938; DAA11718.1; -; Genomic_DNA.\n",
      "DR   PIR; S67686; RNBY2L.\n",
      "DR   RefSeq; NP_010141.1; NM_001180200.1.\n",
      "DR   PDB; 1I3Q; X-ray; 3.10 A; A=1-1733.\n",
      "DR   PDB; 1I50; X-ray; 2.80 A; A=1-1733.\n",
      "DR   PDB; 1I6H; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 1K83; X-ray; 2.80 A; A=1-1733.\n",
      "DR   PDB; 1NIK; X-ray; 4.10 A; A=1-1733.\n",
      "DR   PDB; 1NT9; X-ray; 4.20 A; A=1-1733.\n",
      "DR   PDB; 1PQV; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 1R5U; X-ray; 4.50 A; A=1-1733.\n",
      "DR   PDB; 1R9S; X-ray; 4.25 A; A=1-1733.\n",
      "DR   PDB; 1R9T; X-ray; 3.50 A; A=1-1733.\n",
      "DR   PDB; 1SFO; X-ray; 3.61 A; A=1-1733.\n",
      "DR   PDB; 1TWA; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 1TWC; X-ray; 3.00 A; A=1-1733.\n",
      "DR   PDB; 1TWF; X-ray; 2.30 A; A=1-1733.\n",
      "DR   PDB; 1TWG; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 1TWH; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 1WCM; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 1Y1V; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 1Y1W; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 1Y1Y; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 1Y77; X-ray; 4.50 A; A=1-1733.\n",
      "DR   PDB; 2B63; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 2B8K; X-ray; 4.15 A; A=1-1733.\n",
      "DR   PDB; 2E2H; X-ray; 3.95 A; A=1-1733.\n",
      "DR   PDB; 2E2I; X-ray; 3.41 A; A=1-1733.\n",
      "DR   PDB; 2E2J; X-ray; 3.50 A; A=1-1733.\n",
      "DR   PDB; 2JA5; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 2JA6; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 2JA7; X-ray; 3.80 A; A/M=1-1733.\n",
      "DR   PDB; 2JA8; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 2L0I; NMR; -; B=1675-1688.\n",
      "DR   PDB; 2LO6; NMR; -; B=1675-1688.\n",
      "DR   PDB; 2NVQ; X-ray; 2.90 A; A=1-1733.\n",
      "DR   PDB; 2NVT; X-ray; 3.36 A; A=1-1733.\n",
      "DR   PDB; 2NVX; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 2NVY; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 2NVZ; X-ray; 4.30 A; A=1-1733.\n",
      "DR   PDB; 2R7Z; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 2R92; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 2R93; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 2VUM; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 2YU9; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 3CQZ; X-ray; 2.80 A; A=1-1733.\n",
      "DR   PDB; 3FKI; X-ray; 3.88 A; A=1-1733.\n",
      "DR   PDB; 3GTG; X-ray; 3.78 A; A=1-1733.\n",
      "DR   PDB; 3GTJ; X-ray; 3.42 A; A=1-1733.\n",
      "DR   PDB; 3GTK; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 3GTL; X-ray; 3.38 A; A=1-1733.\n",
      "DR   PDB; 3GTM; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 3GTO; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 3GTP; X-ray; 3.90 A; A=1-1733.\n",
      "DR   PDB; 3GTQ; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 3H3V; X-ray; 4.00 A; B=1-1733.\n",
      "DR   PDB; 3HOU; X-ray; 3.20 A; A/M=1-1733.\n",
      "DR   PDB; 3HOV; X-ray; 3.50 A; A=1-1733.\n",
      "DR   PDB; 3HOW; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 3HOX; X-ray; 3.65 A; A=1-1733.\n",
      "DR   PDB; 3HOY; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 3HOZ; X-ray; 3.65 A; A=1-1733.\n",
      "DR   PDB; 3I4M; X-ray; 3.70 A; A=1-1733.\n",
      "DR   PDB; 3I4N; X-ray; 3.90 A; A=1-1733.\n",
      "DR   PDB; 3J0K; EM; 36.00 A; A=1-1455.\n",
      "DR   PDB; 3J1N; EM; 16.00 A; A=1-1455.\n",
      "DR   PDB; 3K1F; X-ray; 4.30 A; A=1-1733.\n",
      "DR   PDB; 3K7A; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 3M3Y; X-ray; 3.18 A; A=1-1733.\n",
      "DR   PDB; 3M4O; X-ray; 3.57 A; A=1-1733.\n",
      "DR   PDB; 3PO2; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 3PO3; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 3QT1; X-ray; 4.30 A; A=1-1733.\n",
      "DR   PDB; 3RZD; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 3RZO; X-ray; 3.00 A; A=1-1733.\n",
      "DR   PDB; 3S14; X-ray; 2.85 A; A=1-1733.\n",
      "DR   PDB; 3S15; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 3S16; X-ray; 3.24 A; A=1-1733.\n",
      "DR   PDB; 3S17; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 3S1M; X-ray; 3.13 A; A=1-1733.\n",
      "DR   PDB; 3S1N; X-ray; 3.10 A; A=1-1733.\n",
      "DR   PDB; 3S1Q; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 3S1R; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 3S2D; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 3S2H; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 4A3B; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3C; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3D; X-ray; 3.40 A; A=1-1732.\n",
      "DR   PDB; 4A3E; X-ray; 3.40 A; A=1-1732.\n",
      "DR   PDB; 4A3F; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3G; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3I; X-ray; 3.80 A; A=1-1732.\n",
      "DR   PDB; 4A3J; X-ray; 3.70 A; A=1-1732.\n",
      "DR   PDB; 4A3K; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3L; X-ray; 3.50 A; A=1-1732.\n",
      "DR   PDB; 4A3M; X-ray; 3.90 A; A=1-1732.\n",
      "DR   PDB; 4A93; X-ray; 3.40 A; A=1-1732.\n",
      "DR   PDB; 4BBR; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 4BBS; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 4BXX; X-ray; 3.28 A; A=1-1733.\n",
      "DR   PDB; 4BXZ; X-ray; 4.80 A; A=1-1733.\n",
      "DR   PDB; 4BY1; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 4BY7; X-ray; 3.15 A; A=1-1733.\n",
      "DR   PDB; 4GWQ; X-ray; 4.50 A; H=1619-1653.\n",
      "DR   PDB; 4V1M; EM; 6.60 A; A=1-1733.\n",
      "DR   PDB; 4V1N; EM; 7.80 A; A=1-1733.\n",
      "DR   PDB; 4V1O; EM; 9.70 A; A=1-1733.\n",
      "DR   PDB; 4X67; X-ray; 4.10 A; A=1-1733.\n",
      "DR   PDB; 4X6A; X-ray; 3.96 A; A=1-1733.\n",
      "DR   PDB; 4Y52; X-ray; 3.50 A; A=1-1733.\n",
      "DR   PDB; 4Y7N; X-ray; 3.30 A; A=1-1733.\n",
      "DR   PDB; 5C3E; X-ray; 3.70 A; A=1-1733.\n",
      "DR   PDB; 5C44; X-ray; 3.95 A; A=1-1733.\n",
      "DR   PDB; 5C4A; X-ray; 4.20 A; A=1-1733.\n",
      "DR   PDB; 5C4J; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 5C4X; X-ray; 4.00 A; A=1-1733.\n",
      "DR   PDB; 5FMF; EM; 6.00 A; A=1-1733.\n",
      "DR   PDB; 5FYW; EM; 4.35 A; A=1-1733.\n",
      "DR   PDB; 5FZ5; EM; 8.80 A; A=1-1733.\n",
      "DR   PDB; 5IP7; X-ray; 3.52 A; A=2-1733.\n",
      "DR   PDB; 5IP9; X-ray; 3.90 A; A=2-1733.\n",
      "DR   PDB; 5LVF; NMR; -; B=1673-1688.\n",
      "DR   PDB; 5M9D; NMR; -; B=1678-1693.\n",
      "DR   PDB; 5OQJ; EM; 4.70 A; A=1-1733.\n",
      "DR   PDB; 5OQM; EM; 5.80 A; A=1-1733.\n",
      "DR   PDB; 5OT2; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 5SVA; EM; 15.30 A; A=1-1733, k=1666-1690.\n",
      "DR   PDB; 5U5Q; X-ray; 3.80 A; A=1-1733.\n",
      "DR   PDB; 5VKL; X-ray; 2.20 A; B=1476-1498.\n",
      "DR   PDB; 5VKO; X-ray; 1.80 A; B=1468-1500.\n",
      "DR   PDB; 5VVR; EM; 5.80 A; A=1-1733.\n",
      "DR   PDB; 5VVS; EM; 6.40 A; A=1-1733.\n",
      "DR   PDB; 5W4U; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 5W51; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 6BLO; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 6BLP; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 6BM2; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 6BM4; X-ray; 2.95 A; A=1-1733.\n",
      "DR   PDB; 6BQF; X-ray; 3.35 A; A=1-1733.\n",
      "DR   PDB; 6GYK; EM; 5.10 A; A=1-1733.\n",
      "DR   PDB; 6GYL; EM; 4.80 A; A=1-1733.\n",
      "DR   PDB; 6GYM; EM; 6.70 A; A=1-1733.\n",
      "DR   PDB; 6I84; EM; 4.40 A; A=1-1733.\n",
      "DR   PDB; 6NPW; X-ray; 2.49 A; E=1672-1690.\n",
      "DR   PDB; 6O6C; EM; 3.10 A; A=1-1733.\n",
      "DR   PDB; 6UPX; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 6UPY; X-ray; 3.40 A; A=1-1733.\n",
      "DR   PDB; 6UPZ; X-ray; 3.10 A; A=1-1733.\n",
      "DR   PDB; 6UQ0; X-ray; 3.56 A; A=1-1733.\n",
      "DR   PDB; 6UQ1; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 6UQ2; X-ray; 3.20 A; A=1-1733.\n",
      "DR   PDB; 6UQ3; X-ray; 3.47 A; A=1-1733.\n",
      "DR   PDB; 7KED; X-ray; 3.60 A; A=1-1733.\n",
      "DR   PDB; 7KEE; X-ray; 3.45 A; A=1-1733.\n",
      "DR   PDB; 7KEF; X-ray; 3.89 A; A=1-1733.\n",
      "DR   PDB; 7O4I; EM; 3.20 A; A=1-1733.\n",
      "DR   PDB; 7O4J; EM; 2.90 A; A=1-1733.\n",
      "DR   PDB; 7O4K; EM; 3.60 A; A=1-1733.\n",
      "DR   PDB; 7O4L; EM; 3.40 A; A=1-1733.\n",
      "DR   PDB; 7O72; EM; 3.40 A; A=1-1733.\n",
      "DR   PDB; 7O73; EM; 3.40 A; A=1-1733.\n",
      "DR   PDB; 7O75; EM; 3.20 A; A=1-1733.\n",
      "DR   PDBsum; 1I3Q; -.\n",
      "DR   PDBsum; 1I50; -.\n",
      "DR   PDBsum; 1I6H; -.\n",
      "DR   PDBsum; 1K83; -.\n",
      "DR   PDBsum; 1NIK; -.\n",
      "DR   PDBsum; 1NT9; -.\n",
      "DR   PDBsum; 1PQV; -.\n",
      "DR   PDBsum; 1R5U; -.\n",
      "DR   PDBsum; 1R9S; -.\n",
      "DR   PDBsum; 1R9T; -.\n",
      "DR   PDBsum; 1SFO; -.\n",
      "DR   PDBsum; 1TWA; -.\n",
      "DR   PDBsum; 1TWC; -.\n",
      "DR   PDBsum; 1TWF; -.\n",
      "DR   PDBsum; 1TWG; -.\n",
      "DR   PDBsum; 1TWH; -.\n",
      "DR   PDBsum; 1WCM; -.\n",
      "DR   PDBsum; 1Y1V; -.\n",
      "DR   PDBsum; 1Y1W; -.\n",
      "DR   PDBsum; 1Y1Y; -.\n",
      "DR   PDBsum; 1Y77; -.\n",
      "DR   PDBsum; 2B63; -.\n",
      "DR   PDBsum; 2B8K; -.\n",
      "DR   PDBsum; 2E2H; -.\n",
      "DR   PDBsum; 2E2I; -.\n",
      "DR   PDBsum; 2E2J; -.\n",
      "DR   PDBsum; 2JA5; -.\n",
      "DR   PDBsum; 2JA6; -.\n",
      "DR   PDBsum; 2JA7; -.\n",
      "DR   PDBsum; 2JA8; -.\n",
      "DR   PDBsum; 2L0I; -.\n",
      "DR   PDBsum; 2LO6; -.\n",
      "DR   PDBsum; 2NVQ; -.\n",
      "DR   PDBsum; 2NVT; -.\n",
      "DR   PDBsum; 2NVX; -.\n",
      "DR   PDBsum; 2NVY; -.\n",
      "DR   PDBsum; 2NVZ; -.\n",
      "DR   PDBsum; 2R7Z; -.\n",
      "DR   PDBsum; 2R92; -.\n",
      "DR   PDBsum; 2R93; -.\n",
      "DR   PDBsum; 2VUM; -.\n",
      "DR   PDBsum; 2YU9; -.\n",
      "DR   PDBsum; 3CQZ; -.\n",
      "DR   PDBsum; 3FKI; -.\n",
      "DR   PDBsum; 3GTG; -.\n",
      "DR   PDBsum; 3GTJ; -.\n",
      "DR   PDBsum; 3GTK; -.\n",
      "DR   PDBsum; 3GTL; -.\n",
      "DR   PDBsum; 3GTM; -.\n",
      "DR   PDBsum; 3GTO; -.\n",
      "DR   PDBsum; 3GTP; -.\n",
      "DR   PDBsum; 3GTQ; -.\n",
      "DR   PDBsum; 3H3V; -.\n",
      "DR   PDBsum; 3HOU; -.\n",
      "DR   PDBsum; 3HOV; -.\n",
      "DR   PDBsum; 3HOW; -.\n",
      "DR   PDBsum; 3HOX; -.\n",
      "DR   PDBsum; 3HOY; -.\n",
      "DR   PDBsum; 3HOZ; -.\n",
      "DR   PDBsum; 3I4M; -.\n",
      "DR   PDBsum; 3I4N; -.\n",
      "DR   PDBsum; 3J0K; -.\n",
      "DR   PDBsum; 3J1N; -.\n",
      "DR   PDBsum; 3K1F; -.\n",
      "DR   PDBsum; 3K7A; -.\n",
      "DR   PDBsum; 3M3Y; -.\n",
      "DR   PDBsum; 3M4O; -.\n",
      "DR   PDBsum; 3PO2; -.\n",
      "DR   PDBsum; 3PO3; -.\n",
      "DR   PDBsum; 3QT1; -.\n",
      "DR   PDBsum; 3RZD; -.\n",
      "DR   PDBsum; 3RZO; -.\n",
      "DR   PDBsum; 3S14; -.\n",
      "DR   PDBsum; 3S15; -.\n",
      "DR   PDBsum; 3S16; -.\n",
      "DR   PDBsum; 3S17; -.\n",
      "DR   PDBsum; 3S1M; -.\n",
      "DR   PDBsum; 3S1N; -.\n",
      "DR   PDBsum; 3S1Q; -.\n",
      "DR   PDBsum; 3S1R; -.\n",
      "DR   PDBsum; 3S2D; -.\n",
      "DR   PDBsum; 3S2H; -.\n",
      "DR   PDBsum; 4A3B; -.\n",
      "DR   PDBsum; 4A3C; -.\n",
      "DR   PDBsum; 4A3D; -.\n",
      "DR   PDBsum; 4A3E; -.\n",
      "DR   PDBsum; 4A3F; -.\n",
      "DR   PDBsum; 4A3G; -.\n",
      "DR   PDBsum; 4A3I; -.\n",
      "DR   PDBsum; 4A3J; -.\n",
      "DR   PDBsum; 4A3K; -.\n",
      "DR   PDBsum; 4A3L; -.\n",
      "DR   PDBsum; 4A3M; -.\n",
      "DR   PDBsum; 4A93; -.\n",
      "DR   PDBsum; 4BBR; -.\n",
      "DR   PDBsum; 4BBS; -.\n",
      "DR   PDBsum; 4BXX; -.\n",
      "DR   PDBsum; 4BXZ; -.\n",
      "DR   PDBsum; 4BY1; -.\n",
      "DR   PDBsum; 4BY7; -.\n",
      "DR   PDBsum; 4GWQ; -.\n",
      "DR   PDBsum; 4V1M; -.\n",
      "DR   PDBsum; 4V1N; -.\n",
      "DR   PDBsum; 4V1O; -.\n",
      "DR   PDBsum; 4X67; -.\n",
      "DR   PDBsum; 4X6A; -.\n",
      "DR   PDBsum; 4Y52; -.\n",
      "DR   PDBsum; 4Y7N; -.\n",
      "DR   PDBsum; 5C3E; -.\n",
      "DR   PDBsum; 5C44; -.\n",
      "DR   PDBsum; 5C4A; -.\n",
      "DR   PDBsum; 5C4J; -.\n",
      "DR   PDBsum; 5C4X; -.\n",
      "DR   PDBsum; 5FMF; -.\n",
      "DR   PDBsum; 5FYW; -.\n",
      "DR   PDBsum; 5FZ5; -.\n",
      "DR   PDBsum; 5IP7; -.\n",
      "DR   PDBsum; 5IP9; -.\n",
      "DR   PDBsum; 5LVF; -.\n",
      "DR   PDBsum; 5M9D; -.\n",
      "DR   PDBsum; 5OQJ; -.\n",
      "DR   PDBsum; 5OQM; -.\n",
      "DR   PDBsum; 5OT2; -.\n",
      "DR   PDBsum; 5SVA; -.\n",
      "DR   PDBsum; 5U5Q; -.\n",
      "DR   PDBsum; 5VKL; -.\n",
      "DR   PDBsum; 5VKO; -.\n",
      "DR   PDBsum; 5VVR; -.\n",
      "DR   PDBsum; 5VVS; -.\n",
      "DR   PDBsum; 5W4U; -.\n",
      "DR   PDBsum; 5W51; -.\n",
      "DR   PDBsum; 6BLO; -.\n",
      "DR   PDBsum; 6BLP; -.\n",
      "DR   PDBsum; 6BM2; -.\n",
      "DR   PDBsum; 6BM4; -.\n",
      "DR   PDBsum; 6BQF; -.\n",
      "DR   PDBsum; 6GYK; -.\n",
      "DR   PDBsum; 6GYL; -.\n",
      "DR   PDBsum; 6GYM; -.\n",
      "DR   PDBsum; 6I84; -.\n",
      "DR   PDBsum; 6NPW; -.\n",
      "DR   PDBsum; 6O6C; -.\n",
      "DR   PDBsum; 6UPX; -.\n",
      "DR   PDBsum; 6UPY; -.\n",
      "DR   PDBsum; 6UPZ; -.\n",
      "DR   PDBsum; 6UQ0; -.\n",
      "DR   PDBsum; 6UQ1; -.\n",
      "DR   PDBsum; 6UQ2; -.\n",
      "DR   PDBsum; 6UQ3; -.\n",
      "DR   PDBsum; 7KED; -.\n",
      "DR   PDBsum; 7KEE; -.\n",
      "DR   PDBsum; 7KEF; -.\n",
      "DR   PDBsum; 7O4I; -.\n",
      "DR   PDBsum; 7O4J; -.\n",
      "DR   PDBsum; 7O4K; -.\n",
      "DR   PDBsum; 7O4L; -.\n",
      "DR   PDBsum; 7O72; -.\n",
      "DR   PDBsum; 7O73; -.\n",
      "DR   PDBsum; 7O75; -.\n",
      "DR   SASBDB; P04050; -.\n",
      "DR   SMR; P04050; -.\n",
      "DR   BioGRID; 31921; 705.\n",
      "DR   ComplexPortal; CPX-2662; DNA-directed RNA polymerase II complex.\n",
      "DR   DIP; DIP-611N; -.\n",
      "DR   IntAct; P04050; 57.\n",
      "DR   MINT; P04050; -.\n",
      "DR   STRING; 4932.YDL140C; -.\n",
      "DR   CarbonylDB; P04050; -.\n",
      "DR   iPTMnet; P04050; -.\n",
      "DR   MaxQB; P04050; -.\n",
      "DR   PaxDb; P04050; -.\n",
      "DR   PRIDE; P04050; -.\n",
      "DR   TopDownProteomics; P04050; -.\n",
      "DR   EnsemblFungi; YDL140C_mRNA; YDL140C; YDL140C.\n",
      "DR   GeneID; 851415; -.\n",
      "DR   KEGG; sce:YDL140C; -.\n",
      "DR   SGD; S000002299; RPO21.\n",
      "DR   VEuPathDB; FungiDB:YDL140C; -.\n",
      "DR   eggNOG; KOG0260; Eukaryota.\n",
      "DR   GeneTree; ENSGT00930000151033; -.\n",
      "DR   HOGENOM; CLU_000487_3_0_1; -.\n",
      "DR   InParanoid; P04050; -.\n",
      "DR   OMA; LNNAIQM; -.\n",
      "DR   BRENDA; 2.7.7.6; 984.\n",
      "DR   Reactome; R-SCE-113418; Formation of the Early Elongation Complex.\n",
      "DR   Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.\n",
      "DR   Reactome; R-SCE-6781823; Formation of TC-NER Pre-Incision Complex.\n",
      "DR   Reactome; R-SCE-6782135; Dual incision in TC-NER.\n",
      "DR   Reactome; R-SCE-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.\n",
      "DR   Reactome; R-SCE-6796648; TP53 Regulates Transcription of DNA Repair Genes.\n",
      "DR   Reactome; R-SCE-6807505; RNA polymerase II transcribes snRNA genes.\n",
      "DR   Reactome; R-SCE-72086; mRNA Capping.\n",
      "DR   Reactome; R-SCE-73776; RNA Polymerase II Promoter Escape.\n",
      "DR   Reactome; R-SCE-73779; RNA Polymerase II Transcription Pre-Initiation And Promoter Opening.\n",
      "DR   Reactome; R-SCE-75953; RNA Polymerase II Transcription Initiation.\n",
      "DR   Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.\n",
      "DR   Reactome; R-SCE-76042; RNA Polymerase II Transcription Initiation And Promoter Clearance.\n",
      "DR   Reactome; R-SCE-77075; RNA Pol II CTD phosphorylation and interaction with CE.\n",
      "DR   Reactome; R-SCE-9018519; Estrogen-dependent gene expression.\n",
      "DR   EvolutionaryTrace; P04050; -.\n",
      "DR   PRO; PR:P04050; -.\n",
      "DR   Proteomes; UP000002311; Chromosome IV.\n",
      "DR   RNAct; P04050; protein.\n",
      "DR   GO; GO:0010494; C:cytoplasmic stress granule; HDA:SGD.\n",
      "DR   GO; GO:0005739; C:mitochondrion; HDA:SGD.\n",
      "DR   GO; GO:0005634; C:nucleus; IDA:CACAO.\n",
      "DR   GO; GO:0005665; C:RNA polymerase II, core complex; IDA:SGD.\n",
      "DR   GO; GO:0003677; F:DNA binding; IDA:SGD.\n",
      "DR   GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-KW.\n",
      "DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.\n",
      "DR   GO; GO:0006366; P:transcription by RNA polymerase II; IMP:SGD.\n",
      "DR   GO; GO:0001172; P:transcription, RNA-templated; IEA:GOC.\n",
      "DR   GO; GO:0019985; P:translesion synthesis; IMP:SGD.\n",
      "DR   DisProt; DP02527; -.\n",
      "DR   Gene3D; 1.10.132.30; -; 1.\n",
      "DR   Gene3D; 1.10.274.100; -; 1.\n",
      "DR   Gene3D; 3.30.1360.140; -; 1.\n",
      "DR   InterPro; IPR000722; RNA_pol_asu.\n",
      "DR   InterPro; IPR000684; RNA_pol_II_repeat_euk.\n",
      "DR   InterPro; IPR006592; RNA_pol_N.\n",
      "DR   InterPro; IPR007080; RNA_pol_Rpb1_1.\n",
      "DR   InterPro; IPR007066; RNA_pol_Rpb1_3.\n",
      "DR   InterPro; IPR042102; RNA_pol_Rpb1_3_sf.\n",
      "DR   InterPro; IPR007083; RNA_pol_Rpb1_4.\n",
      "DR   InterPro; IPR007081; RNA_pol_Rpb1_5.\n",
      "DR   InterPro; IPR007075; RNA_pol_Rpb1_6.\n",
      "DR   InterPro; IPR007073; RNA_pol_Rpb1_7.\n",
      "DR   InterPro; IPR038593; RNA_pol_Rpb1_7_sf.\n",
      "DR   InterPro; IPR038120; Rpb1_funnel_sf.\n",
      "DR   Pfam; PF04997; RNA_pol_Rpb1_1; 1.\n",
      "DR   Pfam; PF00623; RNA_pol_Rpb1_2; 1.\n",
      "DR   Pfam; PF04983; RNA_pol_Rpb1_3; 1.\n",
      "DR   Pfam; PF05000; RNA_pol_Rpb1_4; 1.\n",
      "DR   Pfam; PF04998; RNA_pol_Rpb1_5; 1.\n",
      "DR   Pfam; PF04992; RNA_pol_Rpb1_6; 1.\n",
      "DR   Pfam; PF04990; RNA_pol_Rpb1_7; 1.\n",
      "DR   Pfam; PF05001; RNA_pol_Rpb1_R; 12.\n",
      "DR   SMART; SM00663; RPOLA_N; 1.\n",
      "DR   PROSITE; PS00115; RNA_POL_II_REPEAT; 22.\n",
      "PE   1: Evidence at protein level;\n",
      "KW   3D-structure; DNA-binding; DNA-directed RNA polymerase; Isopeptide bond;\n",
      "KW   Magnesium; Metal-binding; Nucleotidyltransferase; Nucleus; Phosphoprotein;\n",
      "KW   Reference proteome; Repeat; Transcription; Transferase; Ubl conjugation;\n",
      "KW   Zinc.\n",
      "FT   CHAIN           1..1733\n",
      "FT                   /note=\"DNA-directed RNA polymerase II subunit RPB1\"\n",
      "FT                   /id=\"PRO_0000073946\"\n",
      "FT   REPEAT          1549..1555\n",
      "FT                   /note=\"1\"\n",
      "FT   REPEAT          1556..1562\n",
      "FT                   /note=\"2\"\n",
      "FT   REPEAT          1563..1569\n",
      "FT                   /note=\"3\"\n",
      "FT   REPEAT          1570..1576\n",
      "FT                   /note=\"4\"\n",
      "FT   REPEAT          1577..1583\n",
      "FT                   /note=\"5\"\n",
      "FT   REPEAT          1584..1590\n",
      "FT                   /note=\"6\"\n",
      "FT   REPEAT          1591..1597\n",
      "FT                   /note=\"7\"\n",
      "FT   REPEAT          1598..1604\n",
      "FT                   /note=\"8\"\n",
      "FT   REPEAT          1605..1611\n",
      "FT                   /note=\"9\"\n",
      "FT   REPEAT          1612..1618\n",
      "FT                   /note=\"10\"\n",
      "FT   REPEAT          1619..1625\n",
      "FT                   /note=\"11\"\n",
      "FT   REPEAT          1626..1632\n",
      "FT                   /note=\"12\"\n",
      "FT   REPEAT          1633..1639\n",
      "FT                   /note=\"13\"\n",
      "FT   REPEAT          1640..1646\n",
      "FT                   /note=\"14\"\n",
      "FT   REPEAT          1647..1653\n",
      "FT                   /note=\"15\"\n",
      "FT   REPEAT          1654..1660\n",
      "FT                   /note=\"16\"\n",
      "FT   REPEAT          1661..1667\n",
      "FT                   /note=\"17\"\n",
      "FT   REPEAT          1668..1674\n",
      "FT                   /note=\"18\"\n",
      "FT   REPEAT          1675..1681\n",
      "FT                   /note=\"19\"\n",
      "FT   REPEAT          1682..1688\n",
      "FT                   /note=\"20\"\n",
      "FT   REPEAT          1689..1695\n",
      "FT                   /note=\"21\"\n",
      "FT   REPEAT          1696..1702\n",
      "FT                   /note=\"22\"\n",
      "FT   REPEAT          1703..1709\n",
      "FT                   /note=\"23\"\n",
      "FT   REPEAT          1710..1716\n",
      "FT                   /note=\"24; approximate\"\n",
      "FT   REGION          248..260\n",
      "FT                   /note=\"Lid loop\"\n",
      "FT   REGION          306..323\n",
      "FT                   /note=\"Rudder loop\"\n",
      "FT   REGION          810..822\n",
      "FT                   /note=\"Bridging helix\"\n",
      "FT   REGION          1537..1733\n",
      "FT                   /note=\"Disordered\"\n",
      "FT                   /evidence=\"ECO:0000256|SAM:MobiDB-lite\"\n",
      "FT   REGION          1549..1716\n",
      "FT                   /note=\"C-terminal domain (CTD); 24 X 7 AA approximate\n",
      "FT                   tandem repeats of Y-S-P-T-S-P-[A-S-N-G]\"\n",
      "FT   COMPBIAS        1537..1720\n",
      "FT                   /note=\"Polar residues\"\n",
      "FT                   /evidence=\"ECO:0000256|SAM:MobiDB-lite\"\n",
      "FT   METAL           67\n",
      "FT                   /note=\"Zinc 1\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           70\n",
      "FT                   /note=\"Zinc 1\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           77\n",
      "FT                   /note=\"Zinc 1\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           80\n",
      "FT                   /note=\"Zinc 1; via tele nitrogen\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           107\n",
      "FT                   /note=\"Zinc 2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           110\n",
      "FT                   /note=\"Zinc 2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           148\n",
      "FT                   /note=\"Zinc 2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           167\n",
      "FT                   /note=\"Zinc 2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           481\n",
      "FT                   /note=\"Magnesium 1; catalytic\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           481\n",
      "FT                   /note=\"Magnesium 2; shared with RPB2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           483\n",
      "FT                   /note=\"Magnesium 1; catalytic\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           483\n",
      "FT                   /note=\"Magnesium 2; shared with RPB2\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   METAL           485\n",
      "FT                   /note=\"Magnesium 1; catalytic\"\n",
      "FT                   /evidence=\"ECO:0000269|PubMed:23151482,\n",
      "FT                   ECO:0000269|PubMed:25652824, ECO:0007744|PDB:4BBR,\n",
      "FT                   ECO:0007744|PDB:4V1M\"\n",
      "FT   MOD_RES         1471\n",
      "FT                   /note=\"Phosphothreonine\"\n",
      "FT                   /evidence=\"ECO:0007744|PubMed:18407956\"\n",
      "FT   CROSSLNK        695\n",
      "FT                   /note=\"Glycyl lysine isopeptide (Lys-Gly) (interchain with\n",
      "FT                   G-Cter in ubiquitin)\"\n",
      "FT                   /evidence=\"ECO:0007744|PubMed:22106047\"\n",
      "FT   CROSSLNK        1246\n",
      "FT                   /note=\"Glycyl lysine isopeptide (Lys-Gly) (interchain with\n",
      "FT                   G-Cter in ubiquitin)\"\n",
      "FT                   /evidence=\"ECO:0007744|PubMed:22106047\"\n",
      "FT   CROSSLNK        1350\n",
      "FT                   /note=\"Glycyl lysine isopeptide (Lys-Gly) (interchain with\n",
      "FT                   G-Cter in ubiquitin)\"\n",
      "FT                   /evidence=\"ECO:0007744|PubMed:22106047\"\n",
      "FT   VARIANT         1653..1659\n",
      "FT                   /note=\"Missing (in strain: A364A)\"\n",
      "FT   CONFLICT        1514\n",
      "FT                   /note=\"A -> V (in Ref. 1; CAA26904)\"\n",
      "FT                   /evidence=\"ECO:0000305\"\n",
      "FT   CONFLICT        1524\n",
      "FT                   /note=\"G -> A (in Ref. 1; CAA26904)\"\n",
      "FT                   /evidence=\"ECO:0000305\"\n",
      "FT   CONFLICT        1601\n",
      "FT                   /note=\"T -> M (in Ref. 1)\"\n",
      "FT                   /evidence=\"ECO:0000305\"\n",
      "FT   STRAND          16..18\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           24..29\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          32..34\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6BM4\"\n",
      "FT   STRAND          39..41\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2NVT\"\n",
      "FT   STRAND          43..45\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWC\"\n",
      "FT   STRAND          46..48\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   STRAND          51..54\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          56..58\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          62..64\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3CQZ\"\n",
      "FT   STRAND          67..69\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            74..76\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   STRAND          84..91\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           93..95\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           96..105\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            108..110\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          113..115\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   STRAND          117..119\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2NVQ\"\n",
      "FT   HELIX           120..126\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          127..129\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2E2I\"\n",
      "FT   HELIX           131..142\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          150..152\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          155..157\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   STRAND          160..163\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   STRAND          173..177\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   STRAND          181..185\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          187..190\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          198..202\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           204..211\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          212..214\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S2H\"\n",
      "FT   HELIX           216..221\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            226..228\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           231..234\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          235..239\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            244..246\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          253..255\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          257..260\n",
      "FT                   /evidence=\"ECO:0007829|PDB:4BBR\"\n",
      "FT   HELIX           261..280\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            281..283\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3CQZ\"\n",
      "FT   HELIX           286..304\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          307..310\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   STRAND          313..316\n",
      "FT                   /evidence=\"ECO:0007829|PDB:4BBR\"\n",
      "FT   STRAND          318..321\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   HELIX           325..329\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   TURN            330..335\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           338..340\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          341..344\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6UPZ\"\n",
      "FT   STRAND          347..355\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          363..367\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           368..371\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          375..379\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            382..384\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           385..394\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            395..397\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          398..400\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          402..406\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           408..410\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   STRAND          412..414\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            415..417\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3CQZ\"\n",
      "FT   TURN            419..422\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          431..435\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          441..445\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           452..454\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          455..470\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           472..474\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           475..478\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          482..484\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          486..490\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           495..504\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           507..510\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          511..513\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            514..517\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          518..520\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           525..535\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          536..538\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S1N\"\n",
      "FT   STRAND          540..542\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           543..552\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          553..555\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3CQZ\"\n",
      "FT   STRAND          567..569\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          571..573\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           574..581\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          588..590\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          596..598\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2E2I\"\n",
      "FT   STRAND          600..602\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3PO2\"\n",
      "FT   STRAND          604..608\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          611..615\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           619..622\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          626..628\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   HELIX           629..637\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           639..658\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           666..669\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           673..699\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          706..708\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   HELIX           710..736\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           742..749\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          750..752\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1K83\"\n",
      "FT   HELIX           755..762\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          770..774\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I3Q\"\n",
      "FT   STRAND          778..781\n",
      "FT                   /evidence=\"ECO:0007829|PDB:4BBR\"\n",
      "FT   STRAND          782..784\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            794..798\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            804..806\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           810..845\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          852..854\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6UPY\"\n",
      "FT   STRAND          863..867\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           868..870\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           875..877\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          878..882\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           884..886\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           890..897\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          901..903\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2YU9\"\n",
      "FT   TURN            904..906\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            910..912\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          913..915\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S15\"\n",
      "FT   HELIX           916..919\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           923..946\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            947..949\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          953..958\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           960..970\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          975..977\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1K83\"\n",
      "FT   HELIX           983..994\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1005..1013\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1016..1025\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1028..1033\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1039..1056\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1064..1076\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1079..1082\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S1Q\"\n",
      "FT   HELIX           1086..1088\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2NVQ\"\n",
      "FT   STRAND          1089..1091\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3CQZ\"\n",
      "FT   STRAND          1092..1094\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S1Q\"\n",
      "FT   HELIX           1097..1104\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            1105..1107\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1115..1120\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1122..1126\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1128..1138\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1143..1145\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1147..1154\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1158..1160\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1164..1166\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1167..1171\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1172..1174\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   STRAND          1179..1182\n",
      "FT                   /evidence=\"ECO:0007829|PDB:4BY7\"\n",
      "FT   STRAND          1190..1197\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1199..1204\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1209..1220\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1221..1223\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1224..1228\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1233..1235\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1237..1242\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            1245..1247\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   HELIX           1248..1250\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   HELIX           1258..1270\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1272..1275\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1282..1292\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1296..1310\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1313..1316\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1317..1319\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6UPZ\"\n",
      "FT   TURN            1324..1326\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1328..1330\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1I50\"\n",
      "FT   HELIX           1332..1339\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1341..1357\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            1358..1360\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1365..1374\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   TURN            1375..1377\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1378..1380\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1384..1386\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1388..1390\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1392..1394\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   HELIX           1396..1399\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   TURN            1400..1402\n",
      "FT                   /evidence=\"ECO:0007829|PDB:3S14\"\n",
      "FT   HELIX           1406..1415\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1424..1429\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1437..1439\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   STRAND          1440..1445\n",
      "FT                   /evidence=\"ECO:0007829|PDB:1TWF\"\n",
      "FT   HELIX           1447..1452\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   HELIX           1458..1460\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   HELIX           1463..1466\n",
      "FT                   /evidence=\"ECO:0007829|PDB:6O6C\"\n",
      "FT   HELIX           1474..1476\n",
      "FT                   /evidence=\"ECO:0007829|PDB:5VKO\"\n",
      "FT   STRAND          1677..1680\n",
      "FT                   /evidence=\"ECO:0007829|PDB:2LO6\"\n",
      "FT   STRAND          1689..1691\n",
      "FT                   /evidence=\"ECO:0007829|PDB:5M9D\"\n",
      "SQ   SEQUENCE   1733 AA;  191612 MW;  A45C1360FF99F968 CRC64;\n",
      "     MVGQQYSSAP LRTVKEVQFG LFSPEEVRAI SVAKIRFPET MDETQTRAKI GGLNDPRLGS\n",
      "     IDRNLKCQTC QEGMNECPGH FGHIDLAKPV FHVGFIAKIK KVCECVCMHC GKLLLDEHNE\n",
      "     LMRQALAIKD SKKRFAAIWT LCKTKMVCET DVPSEDDPTQ LVSRGGCGNT QPTIRKDGLK\n",
      "     LVGSWKKDRA TGDADEPELR VLSTEEILNI FKHISVKDFT SLGFNEVFSR PEWMILTCLP\n",
      "     VPPPPVRPSI SFNESQRGED DLTFKLADIL KANISLETLE HNGAPHHAIE EAESLLQFHV\n",
      "     ATYMDNDIAG QPQALQKSGR PVKSIRARLK GKEGRIRGNL MGKRVDFSAR TVISGDPNLE\n",
      "     LDQVGVPKSI AKTLTYPEVV TPYNIDRLTQ LVRNGPNEHP GAKYVIRDSG DRIDLRYSKR\n",
      "     AGDIQLQYGW KVERHIMDND PVLFNRQPSL HKMSMMAHRV KVIPYSTFRL NLSVTSPYNA\n",
      "     DFDGDEMNLH VPQSEETRAE LSQLCAVPLQ IVSPQSNKPC MGIVQDTLCG IRKLTLRDTF\n",
      "     IELDQVLNML YWVPDWDGVI PTPAIIKPKP LWSGKQILSV AIPNGIHLQR FDEGTTLLSP\n",
      "     KDNGMLIIDG QIIFGVVEKK TVGSSNGGLI HVVTREKGPQ VCAKLFGNIQ KVVNFWLLHN\n",
      "     GFSTGIGDTI ADGPTMREIT ETIAEAKKKV LDVTKEAQAN LLTAKHGMTL RESFEDNVVR\n",
      "     FLNEARDKAG RLAEVNLKDL NNVKQMVMAG SKGSFINIAQ MSACVGQQSV EGKRIAFGFV\n",
      "     DRTLPHFSKD DYSPESKGFV ENSYLRGLTP QEFFFHAMGG REGLIDTAVK TAETGYIQRR\n",
      "     LVKALEDIMV HYDNTTRNSL GNVIQFIYGE DGMDAAHIEK QSLDTIGGSD AAFEKRYRVD\n",
      "     LLNTDHTLDP SLLESGSEIL GDLKLQVLLD EEYKQLVKDR KFLREVFVDG EANWPLPVNI\n",
      "     RRIIQNAQQT FHIDHTKPSD LTIKDIVLGV KDLQENLLVL RGKNEIIQNA QRDAVTLFCC\n",
      "     LLRSRLATRR VLQEYRLTKQ AFDWVLSNIE AQFLRSVVHP GEMVGVLAAQ SIGEPATQMT\n",
      "     LNTFHFAGVA SKKVTSGVPR LKEILNVAKN MKTPSLTVYL EPGHAADQEQ AKLIRSAIEH\n",
      "     TTLKSVTIAS EIYYDPDPRS TVIPEDEEII QLHFSLLDEE AEQSFDQQSP WLLRLELDRA\n",
      "     AMNDKDLTMG QVGERIKQTF KNDLFVIWSE DNDEKLIIRC RVVRPKSLDA ETEAEEDHML\n",
      "     KKIENTMLEN ITLRGVENIE RVVMMKYDRK VPSPTGEYVK EPEWVLETDG VNLSEVMTVP\n",
      "     GIDPTRIYTN SFIDIMEVLG IEAGRAALYK EVYNVIASDG SYVNYRHMAL LVDVMTTQGG\n",
      "     LTSVTRHGFN RSNTGALMRC SFEETVEILF EAGASAELDD CRGVSENVIL GQMAPIGTGA\n",
      "     FDVMIDEESL VKYMPEQKIT EIEDGQDGGV TPYSNESGLV NADLDVKDEL MFSPLVDSGS\n",
      "     NDAMAGGFTA YGGADYGEAT SPFGAYGEAP TSPGFGVSSP GFSPTSPTYS PTSPAYSPTS\n",
      "     PSYSPTSPSY SPTSPSYSPT SPSYSPTSPS YSPTSPSYSP TSPSYSPTSP SYSPTSPSYS\n",
      "     PTSPSYSPTS PSYSPTSPSY SPTSPSYSPT SPSYSPTSPA YSPTSPSYSP TSPSYSPTSP\n",
      "     SYSPTSPSYS PTSPNYSPTS PSYSPTSPGY SPGSPAYSPK QDEQKHNENE NSR\n",
      "//\n",
      "\n"
     ]
    }
   ],
   "source": [
    "import requests\n",
    "\n",
    "URL = \"https://www.uniprot.org\"\n",
    "\n",
    "# Find a single protein\n",
    "r = requests.get(\"{}/uniprot/P04050.txt\".format(URL))  # Without extension, it will look at the 'Accept' header\n",
    "print(r.status_code)\n",
    "print(r.text)\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "f23a8602",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "Q96NG5\n",
      "Q6ZN19\n",
      "Q9UI25\n",
      "Q86XN6\n",
      "A8MUZ8\n",
      "Q08ER8\n",
      "Q9GZX5\n",
      "Q9GZP7\n",
      "Q3MJ13\n",
      "Q9NY84\n",
      "B1APH4\n",
      "Q9HBT8\n",
      "Q76KX8\n",
      "Q96E35\n",
      "P3\n"
     ]
    }
   ],
   "source": [
    "# Make a query\n",
    "r = requests.get(\"{}/uniprot/?query=reviewed:yes+AND+organism:\\\"homo sapiens\\\"&format=list\".format(URL))\n",
    "print(r.status_code)\n",
    "print(r.text[:100])\n",
    "r_name = set(r.text.strip().split(\"\\n\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "d4c74b23",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200 200\n",
      "{'D4N3P2', 'P84351', 'D4N3P3'}\n",
      "set()\n"
     ]
    }
   ],
   "source": [
    "# Why we get a different number of proteins using 9606 instead of \"homo sapiens\" in the organism field?\n",
    "r_name = requests.get(\"{}/uniprot/?query=reviewed:yes+AND+organism:\\\"homo sapiens\\\"&format=list\".format(URL))\n",
    "r_taxon = requests.get(\"{}/uniprot/?query=reviewed:yes+AND+organism:9606&format=list\".format(URL))\n",
    "print(r_name.status_code, r_taxon.status_code)\n",
    "\n",
    "r_name = set(r_name.text.strip().split(\"\\n\"))\n",
    "r_taxon = set(r_taxon.text.strip().split(\"\\n\"))\n",
    "print(r_name - r_taxon, r_taxon - r_name, sep=\"\\n\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "acc7309b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "200\n",
      "From\tTo\n",
      "P04050\t1I3Q\n",
      "P04050\t1I50\n",
      "P04050\t1I6H\n",
      "P04050\t1K83\n",
      "P04050\t1NIK\n",
      "P04050\t1NT9\n",
      "P04050\t1PQV\n",
      "P04050\t1R5U\n",
      "P04050\t1R9S\n",
      "P04050\t1R9T\n",
      "P04050\t1SFO\n",
      "P04050\t1TWA\n",
      "P04050\t1TWC\n",
      "P04050\t1TWF\n",
      "P04050\t1TWG\n",
      "P04050\t1TWH\n",
      "P04050\t1WCM\n",
      "P04050\t1Y1V\n",
      "P04050\t1Y1W\n",
      "P04050\t1Y1Y\n",
      "P04050\t1Y77\n",
      "P04050\t2B63\n",
      "P04050\t2B8K\n",
      "P04050\t2E2H\n",
      "P04050\t2E2I\n",
      "P04050\t2E2J\n",
      "P04050\t2JA5\n",
      "P04050\t2JA6\n",
      "P04050\t2JA7\n",
      "P04050\t2JA8\n",
      "P04050\t2L0I\n",
      "P04050\t2LO6\n",
      "P04050\t2NVQ\n",
      "P04050\t2NVT\n",
      "P04050\t2NVX\n",
      "P04050\t2NVY\n",
      "P04050\t2NVZ\n",
      "P04050\t2R7Z\n",
      "P04050\t2R92\n",
      "P04050\t2R93\n",
      "P04050\t2VUM\n",
      "P04050\t2YU9\n",
      "P04050\t3CQZ\n",
      "P04050\t3FKI\n",
      "P04050\t3GTG\n",
      "P04050\t3GTJ\n",
      "P04050\t3GTK\n",
      "P04050\t3GTL\n",
      "P04050\t3GTM\n",
      "P04050\t3GTO\n",
      "P04050\t3GTP\n",
      "P04050\t3GTQ\n",
      "P04050\t3H3V\n",
      "P04050\t3HOU\n",
      "P04050\t3HOV\n",
      "P04050\t3HOW\n",
      "P04050\t3HOX\n",
      "P04050\t3HOY\n",
      "P04050\t3HOZ\n",
      "P04050\t3I4M\n",
      "P04050\t3I4N\n",
      "P04050\t3J0K\n",
      "P04050\t3J1N\n",
      "P04050\t3K1F\n",
      "P04050\t3K7A\n",
      "P04050\t3M3Y\n",
      "P04050\t3M4O\n",
      "P04050\t3PO2\n",
      "P04050\t3PO3\n",
      "P04050\t3QT1\n",
      "P04050\t3RZD\n",
      "P04050\t3RZO\n",
      "P04050\t3S14\n",
      "P04050\t3S15\n",
      "P04050\t3S16\n",
      "P04050\t3S17\n",
      "P04050\t3S1M\n",
      "P04050\t3S1N\n",
      "P04050\t3S1Q\n",
      "P04050\t3S1R\n",
      "P04050\t3S2D\n",
      "P04050\t3S2H\n",
      "P04050\t4A3B\n",
      "P04050\t4A3C\n",
      "P04050\t4A3D\n",
      "P04050\t4A3E\n",
      "P04050\t4A3F\n",
      "P04050\t4A3G\n",
      "P04050\t4A3I\n",
      "P04050\t4A3J\n",
      "P04050\t4A3K\n",
      "P04050\t4A3L\n",
      "P04050\t4A3M\n",
      "P04050\t4A93\n",
      "P04050\t4BBR\n",
      "P04050\t4BBS\n",
      "P04050\t4BXX\n",
      "P04050\t4BXZ\n",
      "P04050\t4BY1\n",
      "P04050\t4BY7\n",
      "P04050\t4GWQ\n",
      "P04050\t4V1M\n",
      "P04050\t4V1N\n",
      "P04050\t4V1O\n",
      "P04050\t4X67\n",
      "P04050\t4X6A\n",
      "P04050\t4Y52\n",
      "P04050\t4Y7N\n",
      "P04050\t5C3E\n",
      "P04050\t5C44\n",
      "P04050\t5C4A\n",
      "P04050\t5C4J\n",
      "P04050\t5C4X\n",
      "P04050\t5FMF\n",
      "P04050\t5FYW\n",
      "P04050\t5FZ5\n",
      "P04050\t5IP7\n",
      "P04050\t5IP9\n",
      "P04050\t5LVF\n",
      "P04050\t5M9D\n",
      "P04050\t5OQJ\n",
      "P04050\t5OQM\n",
      "P04050\t5OT2\n",
      "P04050\t5SVA\n",
      "P04050\t5U5Q\n",
      "P04050\t5VKL\n",
      "P04050\t5VKO\n",
      "P04050\t5VVR\n",
      "P04050\t5VVS\n",
      "P04050\t5W4U\n",
      "P04050\t5W51\n",
      "P04050\t6BLO\n",
      "P04050\t6BLP\n",
      "P04050\t6BM2\n",
      "P04050\t6BM4\n",
      "P04050\t6BQF\n",
      "P04050\t6GYK\n",
      "P04050\t6GYL\n",
      "P04050\t6GYM\n",
      "P04050\t6I84\n",
      "P04050\t6NPW\n",
      "P04050\t6O6C\n",
      "P04050\t6UPX\n",
      "P04050\t6UPY\n",
      "P04050\t6UPZ\n",
      "P04050\t6UQ0\n",
      "P04050\t6UQ1\n",
      "P04050\t6UQ2\n",
      "P04050\t6UQ3\n",
      "P04050\t7KED\n",
      "P04050\t7KEE\n",
      "P04050\t7KEF\n",
      "P04050\t7O4I\n",
      "P04050\t7O4J\n",
      "P04050\t7O4K\n",
      "P04050\t7O4L\n",
      "P04050\t7O72\n",
      "P04050\t7O73\n",
      "P04050\t7O75\n",
      "P04637\t1A1U\n",
      "P04637\t1AIE\n",
      "P04637\t1C26\n",
      "P04637\t1DT7\n",
      "P04637\t1GZH\n",
      "P04637\t1H26\n",
      "P04637\t1HS5\n",
      "P04637\t1JSP\n",
      "P04637\t1KZY\n",
      "P04637\t1MA3\n",
      "P04637\t1OLG\n",
      "P04637\t1OLH\n",
      "P04637\t1PES\n",
      "P04637\t1PET\n",
      "P04637\t1SAE\n",
      "P04637\t1SAF\n",
      "P04637\t1SAK\n",
      "P04637\t1SAL\n",
      "P04637\t1TSR\n",
      "P04637\t1TUP\n",
      "P04637\t1UOL\n",
      "P04637\t1XQH\n",
      "P04637\t1YC5\n",
      "P04637\t1YCQ\n",
      "P04637\t1YCR\n",
      "P04637\t1YCS\n",
      "P04637\t2AC0\n",
      "P04637\t2ADY\n",
      "P04637\t2AHI\n",
      "P04637\t2ATA\n",
      "P04637\t2B3G\n",
      "P04637\t2BIM\n",
      "P04637\t2BIN\n",
      "P04637\t2BIO\n",
      "P04637\t2BIP\n",
      "P04637\t2BIQ\n",
      "P04637\t2F1X\n",
      "P04637\t2FEJ\n",
      "P04637\t2FOJ\n",
      "P04637\t2FOO\n",
      "P04637\t2GS0\n",
      "P04637\t2H1L\n",
      "P04637\t2H2D\n",
      "P04637\t2H2F\n",
      "P04637\t2H4F\n",
      "P04637\t2H4H\n",
      "P04637\t2H4J\n",
      "P04637\t2H59\n",
      "P04637\t2J0Z\n",
      "P04637\t2J10\n",
      "P04637\t2J11\n",
      "P04637\t2J1W\n",
      "P04637\t2J1X\n",
      "P04637\t2J1Y\n",
      "P04637\t2J1Z\n",
      "P04637\t2J20\n",
      "P04637\t2J21\n",
      "P04637\t2K8F\n",
      "P04637\t2L14\n",
      "P04637\t2LY4\n",
      "P04637\t2MEJ\n",
      "P04637\t2MWO\n",
      "P04637\t2MWP\n",
      "P04637\t2MWY\n",
      "P04637\t2MZD\n",
      "P04637\t2OCJ\n",
      "P04637\t2PCX\n",
      "P04637\t2RUK\n",
      "P04637\t2VUK\n",
      "P04637\t2WGX\n",
      "P04637\t2X0U\n",
      "P04637\t2X0V\n",
      "P04637\t2X0W\n",
      "P04637\t2XWR\n",
      "P04637\t2YBG\n",
      "P04637\t2YDR\n",
      "P04637\t2Z5S\n",
      "P04637\t2Z5T\n",
      "P04637\t3D05\n",
      "P04637\t3D06\n",
      "P04637\t3D07\n",
      "P04637\t3D08\n",
      "P04637\t3D09\n",
      "P04637\t3D0A\n",
      "P04637\t3DAB\n",
      "P04637\t3DAC\n",
      "P04637\t3IGK\n",
      "P04637\t3IGL\n",
      "P04637\t3KMD\n",
      "P04637\t3KZ8\n",
      "P04637\t3LW1\n",
      "P04637\t3OQ5\n",
      "P04637\t3PDH\n",
      "P04637\t3Q01\n",
      "P04637\t3Q05\n",
      "P04637\t3Q06\n",
      "P04637\t3SAK\n",
      "P04637\t3TG5\n",
      "P04637\t3TS8\n",
      "P04637\t3ZME\n",
      "P04637\t4AGL\n",
      "P04637\t4AGM\n",
      "P04637\t4AGN\n",
      "P04637\t4AGO\n",
      "P04637\t4AGP\n",
      "P04637\t4AGQ\n",
      "P04637\t4BUZ\n",
      "P04637\t4BV2\n",
      "P04637\t4HFZ\n",
      "P04637\t4HJE\n",
      "P04637\t4IBQ\n",
      "P04637\t4IBS\n",
      "P04637\t4IBT\n",
      "P04637\t4IBU\n",
      "P04637\t4IBV\n",
      "P04637\t4IBW\n",
      "P04637\t4IBY\n",
      "P04637\t4IBZ\n",
      "P04637\t4IJT\n",
      "P04637\t4KVP\n",
      "P04637\t4LO9\n",
      "P04637\t4LOE\n",
      "P04637\t4LOF\n",
      "P04637\t4MZI\n",
      "P04637\t4MZR\n",
      "P04637\t4QO1\n",
      "P04637\t4RP6\n",
      "P04637\t4RP7\n",
      "P04637\t4X34\n",
      "P04637\t4XR8\n",
      "P04637\t4ZZJ\n",
      "P04637\t5A7B\n",
      "P04637\t5AB9\n",
      "P04637\t5ABA\n",
      "P04637\t5AOI\n",
      "P04637\t5AOJ\n",
      "P04637\t5AOK\n",
      "P04637\t5AOL\n",
      "P04637\t5AOM\n",
      "P04637\t5BUA\n",
      "P04637\t5ECG\n",
      "P04637\t5G4M\n",
      "P04637\t5G4N\n",
      "P04637\t5G4O\n",
      "P04637\t5HOU\n",
      "P04637\t5HP0\n",
      "P04637\t5HPD\n",
      "P04637\t5LAP\n",
      "P04637\t5LGY\n",
      "P04637\t5MCT\n",
      "P04637\t5MCU\n",
      "P04637\t5MCV\n",
      "P04637\t5MCW\n",
      "P04637\t5MF7\n",
      "P04637\t5MG7\n",
      "P04637\t5MHC\n",
      "P04637\t5MOC\n",
      "P04637\t5O1A\n",
      "P04637\t5O1B\n",
      "P04637\t5O1C\n",
      "P04637\t5O1D\n",
      "P04637\t5O1E\n",
      "P04637\t5O1F\n",
      "P04637\t5O1G\n",
      "P04637\t5O1H\n",
      "P04637\t5O1I\n",
      "P04637\t5OL0\n",
      "P04637\t5UN8\n",
      "P04637\t5XZC\n",
      "P04637\t6FF9\n",
      "P04637\t6FJ5\n",
      "P04637\t6GGA\n",
      "P04637\t6GGB\n",
      "P04637\t6GGC\n",
      "P04637\t6GGD\n",
      "P04637\t6GGE\n",
      "P04637\t6GGF\n",
      "P04637\t6LHD\n",
      "P04637\t6R5L\n",
      "P04637\t6RJZ\n",
      "P04637\t6RK8\n",
      "P04637\t6RKI\n",
      "P04637\t6RKK\n",
      "P04637\t6RKM\n",
      "P04637\t6RL3\n",
      "P04637\t6RL4\n",
      "P04637\t6RL6\n",
      "P04637\t6RM5\n",
      "P04637\t6RM7\n",
      "P04637\t6RWH\n",
      "P04637\t6RWI\n",
      "P04637\t6RWS\n",
      "P04637\t6RWU\n",
      "P04637\t6RX2\n",
      "P04637\t6RZ3\n",
      "P04637\t6S39\n",
      "P04637\t6S3C\n",
      "P04637\t6S40\n",
      "P04637\t6S9Q\n",
      "P04637\t6SHZ\n",
      "P04637\t6SI0\n",
      "P04637\t6SI1\n",
      "P04637\t6SI2\n",
      "P04637\t6SI3\n",
      "P04637\t6SI4\n",
      "P04637\t6SIN\n",
      "P04637\t6SIO\n",
      "P04637\t6SIP\n",
      "P04637\t6SIQ\n",
      "P04637\t6SL6\n",
      "P04637\t6SLV\n",
      "P04637\t6T58\n",
      "P04637\t6V4F\n",
      "P04637\t6V4H\n",
      "P04637\t6VQO\n",
      "P04637\t6VR1\n",
      "P04637\t6VR5\n",
      "P04637\t6VRM\n",
      "P04637\t6VRN\n",
      "P04637\t6W51\n",
      "P04637\t6XRE\n",
      "P04637\t7BWN\n",
      "P04637\t7DHY\n",
      "P04637\t7DHZ\n",
      "P04637\t7EL4\n",
      "\n"
     ]
    }
   ],
   "source": [
    "# Find UniProt/UniRef\n",
    "r = requests.get(\"{}/uploadlists/\".format(URL), params={'from': 'ACC', \n",
    "                                                        'to': 'PDB_ID', \n",
    "                                                        'format': 'tab', \n",
    "                                                        'query': 'P04050 P04637'})\n",
    "print(r.status_code)\n",
    "print(r.text)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "85cee86b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[({'type': 'scientific'}, 'Saccharomyces cerevisiae (strain ATCC 204508 / S288c)'), ({'type': 'common'}, \"Baker's yeast\")]\n"
     ]
    }
   ],
   "source": [
    "# Working with XML\n",
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "r = requests.get(\"{}/uniprot/P33313.xml\".format(URL))  # Without extension, it will look at the 'Accept' header\n",
    "# print(r.text[:1000])\n",
    "\n",
    "NS = {'uniprot': 'http://uniprot.org/uniprot'}\n",
    "root = ET.fromstring(r.text)\n",
    "\n",
    "print([(ele.attrib, ele.text) for ele in root.findall(\"uniprot:entry/uniprot:organism/uniprot:name\", NS)])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "id": "4680fb30",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'type': 'GO', 'id': 'GO:0005737'}\n",
      "{'type': 'term', 'value': 'C:cytoplasm'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000353'}\n",
      "{'type': 'project', 'value': 'SGD'}\n",
      "{'type': 'GO', 'id': 'GO:0030544'}\n",
      "{'type': 'term', 'value': 'F:Hsp70 protein binding'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000314'}\n",
      "{'type': 'project', 'value': 'SGD'}\n",
      "{'type': 'GO', 'id': 'GO:0051879'}\n",
      "{'type': 'term', 'value': 'F:Hsp90 protein binding'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000314'}\n",
      "{'type': 'project', 'value': 'SGD'}\n",
      "{'type': 'GO', 'id': 'GO:0043022'}\n",
      "{'type': 'term', 'value': 'F:ribosome binding'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000314'}\n",
      "{'type': 'project', 'value': 'SGD'}\n",
      "{'type': 'GO', 'id': 'GO:0006457'}\n",
      "{'type': 'term', 'value': 'P:protein folding'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000353'}\n",
      "{'type': 'project', 'value': 'SGD'}\n",
      "{'type': 'GO', 'id': 'GO:0042026'}\n",
      "{'type': 'term', 'value': 'P:protein refolding'}\n",
      "{'type': 'evidence', 'value': 'ECO:0000316'}\n",
      "{'type': 'project', 'value': 'SGD'}\n"
     ]
    }
   ],
   "source": [
    "# Find GO terms annotated to P33313\n",
    "\n",
    "\n",
    "r = requests.get(\"{}/uniprot/P33313.xml\".format(URL))  # Without extension, it will look at the 'Accept' header\n",
    "NS = {'uniprot': 'http://uniprot.org/uniprot'}\n",
    "root = ET.fromstring(r.text)\n",
    "\n",
    "for ele in root.findall(\"uniprot:entry/uniprot:dbReference\", NS):\n",
    "    if ele.attrib[\"type\"] == \"GO\":\n",
    "        print(ele.attrib)\n",
    "        for ele2 in ele.findall(\"uniprot:property\", NS):\n",
    "            print(ele2.attrib)\n",
    "#             if ele2.attrib[\"type\"] == \"chains\":\n",
    "#                 chains = ele2.attrib[\"value\"].split(\", \")\n",
    "#                 for chain in chains:\n",
    "#                     ch, pos = chain.split(\"=\")\n",
    "#                     start, end = pos.split(\"-\")\n",
    "#                     start = int(start)\n",
    "#                     end = int(end)\n",
    "#                     print(ch, start, end)\n",
    "                    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "64d98c67",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "{'type': 'PDB', 'id': '6HFM'}\n",
      "A/B 221 385\n",
      "{'type': 'PDB', 'id': '6HFT'}\n",
      "A 70 385\n",
      "[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]\n",
      "0.42857142857142855\n"
     ]
    }
   ],
   "source": [
    "# Find the fraction of residues covered by PDB structures in P33313. How many residues are covered by at least 2 structures?\n",
    "\n",
    "r = requests.get(\"{}/uniprot/P33313.xml\".format(URL))  # Without extension, it will look at the 'Accept' header\n",
    "NS = {'uniprot': 'http://uniprot.org/uniprot'}\n",
    "root = ET.fromstring(r.text)\n",
    "\n",
    "sequence_length = int(root.find(\"uniprot:entry/uniprot:sequence\", NS).attrib[\"length\"])\n",
    "\n",
    "sequence_state = [0] * sequence_length\n",
    "for ele in root.findall(\"uniprot:entry/uniprot:dbReference\", NS):\n",
    "    if ele.attrib[\"type\"] == \"PDB\":\n",
    "        print(ele.attrib)\n",
    "        for ele2 in ele.findall(\"uniprot:property\", NS):\n",
    "            if ele2.attrib[\"type\"] == \"chains\":\n",
    "                chains = ele2.attrib[\"value\"].split(\", \")\n",
    "                for chain in chains:\n",
    "                    ch, pos = chain.split(\"=\")\n",
    "                    start, end = pos.split(\"-\")\n",
    "                    start = int(start)\n",
    "                    end = int(end)\n",
    "                    print(ch, start, end)\n",
    "                    \n",
    "                    # For each sequence position count the number of PDB structures covering that residue\n",
    "                    for i in range(start - 1, end):\n",
    "                        sequence_state[i] += 1\n",
    "\n",
    "# PDB coverage for each sequence residues\n",
    "print(sequence_state)\n",
    "\n",
    "# Fraction of sequence residues covered by PDB structures\n",
    "print(sum([1 for r in sequence_state if r > 1]) / len(sequence_state))"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.9.7"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}