Structure of PDB 2b63 Chain B Binding Site BS01

Receptor Information
>2b63 Chain B (length=1112) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAF
FLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK
DIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLN
RYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNG
VWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVY
RPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYI
DAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMIL
GVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYP
QKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRG
LFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI
APGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLK
FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLII
NPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREH
GYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ
VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI
CGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNI
TPRLYTDRSRDF
Ligand information
>2b63 Chain R (length=31) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cagcacugauugcggucgagguagcuugaug
..<<<.....>>>.<<<<<<....>>>>>>.
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2b63 Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs
Resolution3.8 Å
Binding residue
(original residue number in PDB)		Y459 T463 N465 S474 S475 R476 Q481 V482 R512 Q531 R1124
Binding residue
(residue number reindexed from 1)		Y375 T379 N381 S390 S391 R392 Q397 V398 R428 Q447 R1012
Binding affinityPDBbind-CN: Kd=33nM
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D738
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:2b63, PDBe:2b63, PDBj:2b63
PDBsum2b63
PubMed16341226
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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