Structure of PDB 5c44 Chain A Binding Site BS02

Receptor Information
>5c44 Chain A (length=1434) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIG
GLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKK
VCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETD
VPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRV
LSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSIS
FNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVA
TYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSART
VISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPG
AKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLH
KMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAEL
SQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLY
WVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPK
DNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQK
VVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANL
LTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGS
KGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVE
NSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVH
YDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDL
LNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGE
ANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLR
GKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEA
QFLRSVVHPGEMVGVLAAQSIGEPATQMTLFHFAGVASKKVTSGVPRLKE
ILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIY
YDPDPRSTVIPEDEEIIQLHFSFDQQSPWLLRLELDRAAMNDKDLTMGQV
GERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPAEEDHMLKKIENTMLEN
ITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVP
GIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMAL
LVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDD
CRGVSENVILGQMAPIGTGAFDVMIDEESLVKYM
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5c44 Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.
Resolution3.95 Å
Binding residue
(original residue number in PDB)		K330 K332 R337 R344 R350 Q447 P448 A832 G835 Y836 R1386 E1403 E1404
Binding residue
(residue number reindexed from 1)		K329 K331 R336 R343 R349 Q446 P447 A831 G834 Y835 R1366 E1383 E1384
Enzymatic activity
Catalytic site (original residue number in PDB) D481 D483 D485 H1085
Catalytic site (residue number reindexed from 1) D480 D482 D484 H1082
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
GO:0019985 translesion synthesis
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5c44, PDBe:5c44, PDBj:5c44
PDBsum5c44
PubMed26186291
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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