Structure of PDB 6gyl Chain B

Receptor sequence
>6gylB (length=1152) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSS
GLFVDVKKRTYELKYELGKVFIGRLPIMLRSKNCYLSEATESDLYKLKEC
PFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALE
KGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDG
EILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKK
EKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQ
DDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMK
LAINAKTITSGLKYALATGNWGSSRAGVSQVLNRYTYSSTLSHLRRTNTP
IAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITF
LSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKG
DINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGH
IAKLMATEYQDDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPA
EVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQS
AMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQ
NAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSIT
ETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPD
EEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTT
KIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRM
TVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEV
MYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEG
RSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTV
IAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRS
RD
3D structure
PDB6gyl Promoter Distortion and Opening in the RNA Polymerase II Cleft.
ChainB
Resolution4.8 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) D766
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 ZN B C1163 C1182 C1092 C1111
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:6gyl, PDBe:6gyl, PDBj:6gyl
PDBsum6gyl
PubMed30472190
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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