Structure of PDB 5vvr Chain B

Receptor sequence
>5vvrB (length=1207) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDS
TLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEA
RLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQL
EGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF
KTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWG
EQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNT
HWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLE
DYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIR
DIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQ
DIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANE
ENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRN
TYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL
PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYG
MSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP
ISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ
PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICG
LMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDRSRDF
3D structure
PDB5vvr Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
ChainB
Resolution5.8 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D820
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna B I251 R430 I502 R504 I234 R413 I485 R487
BS02 dna B Y866 E923 R1122 R1129 Y849 E906 R1105 R1112
BS03 ZN B C1163 C1166 C1185 C1146 C1149 C1168
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003729 mRNA 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:0032549 ribonucleoside binding
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
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
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:5vvr, PDBe:5vvr, PDBj:5vvr
PDBsum5vvr
PubMed29168508
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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