Structure of PDB 4v1m Chain B Binding Site BS03

Receptor Information
>4v1m Chain B (length=1156) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL
RNLTYSSGLFVDVKKRTYEAIDELKYELGKVFIGRLPIMLRSKNCYLSEA
TESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPI
SHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVI
IFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFI
GRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINR
LLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQR
TVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLN
RYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS
LMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVH
RNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIV
EDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEE
SILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASI
IPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGT
TRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLF
FRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRV
SGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRV
RTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIP
SRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRG
FEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQP
VEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGL
MTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYT
DRSRDF
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4v1m Chain B Residue 2225 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4v1m Architecture of the RNA Polymerase II-Mediator Core Initiation Complex.
Resolution6.6 Å
Binding residue
(original residue number in PDB)		C1163 C1185
Binding residue
(residue number reindexed from 1)		C1095 C1117
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D782
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: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
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Cellular Component
External links
PDB RCSB:4v1m, PDBe:4v1m, PDBj:4v1m
PDBsum4v1m
PubMed25652824
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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