Structure of PDB 8ceo Chain B Binding Site BS01

Receptor Information
>8ceo Chain B (length=1180) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDS
TLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEA
RLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEGKVFIGRLPI
MLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNI
VQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKAT
LPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGF
VIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFES
RKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFK
KLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGERAGV
SQVLNRYTYSSTLSHLRRTNTPIGKLAKPRQLHNTHWGLVCPAETPEGQA
CGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFV
NGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGR
VYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIDVEEYTWSSLLNE
GLVEYIDAEEEESILIAMQPEDLEPAEDVDPAKRIRVSHHATTFTHCEIH
PSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMAN
ILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQS
SIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLD
DDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRST
ENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITY
RREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDA
SPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQR
LRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAA
SFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQI
HIPYAAKLLFQELMAMNITPRLYTDRSRDF
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 chain8ceo Chain B Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ceo Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		C1166 C1182 C1185
Binding residue
(residue number reindexed from 1)		C1122 C1138 C1141
Annotation score1
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: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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ceo, PDBe:8ceo, PDBj:8ceo
PDBsum8ceo
PubMed37014863
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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