Structure of PDB 6upy Chain A Binding Site BS03

Receptor Information
>6upy Chain A (length=1384) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGG
LNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKV
CECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDV
PLVSRGGCGNTQPTIRKDGLKLVGSWKLRVLSTEEILNIFKHISVKDFTS
LGFNEVFSRPEWMILTCLPVPPPPVRPSRGEDDLTFKLADILKANISLET
LEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQAGRPVKSIRARLKGK
EGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTP
YNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKV
ERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADF
DGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIR
KLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAI
PNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHV
VTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITET
IAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRL
AEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDR
TLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTA
ETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQS
LDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEE
YKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLT
IKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVL
QEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLK
KVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTT
LKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLQQSPWLLRLELDRAAM
NDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVAEEDHMLKK
IENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVN
LSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSY
VNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEA
GASAELDDCRGVSENVILGQMAPIGTGAFDVMID
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6upy RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
Resolution3.4 Å
Binding residue
(original residue number in PDB)		K101 W139 K143 K1109 N1110 H1387
Binding residue
(residue number reindexed from 1)		K99 W137 K141 K1067 N1068 H1325
Enzymatic activity
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
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Cellular Component
External links
PDB RCSB:6upy, PDBe:6upy, PDBj:6upy
PDBsum6upy
PubMed32284409
UniProtP04050|RPB1_YEAST DNA-directed RNA polymerase II subunit RPB1 (Gene Name=RPO21)

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