Structure of PDB 6bm2 Chain B Binding Site BS03

Receptor Information
>6bm2 Chain B (length=1097) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATL
PYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFV
IQDRETALDFIGRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLG
YMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF
RYMQRTLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYS
STLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI
SVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPAR
LMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDES
LGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIA
MQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQ
SPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLK
FRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQE
KKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIG
KTTPITAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKI
PQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTV
AHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMY
NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS
RDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIA
KLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
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 chain6bm2 Chain B Residue 1301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6bm2 Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
Resolution3.403 Å
Binding residue
(original residue number in PDB)		C1163 C1166
Binding residue
(residue number reindexed from 1)		C1040 C1043
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D724
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6bm2, PDBe:6bm2, PDBj:6bm2
PDBsum6bm2
PubMed29487211
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

[Back to BioLiP]