Structure of PDB 6wvk Chain D Binding Site BS03

Receptor Information
>6wvk Chain D (length=1184) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFG
PTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSH
IWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEK
EYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRR
TRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGR
PVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMY
QCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLES
VIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGD
QMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLT
LERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQ
RSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVK
AVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTK
AGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVIS
IWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMAN
PAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRR
LVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVK
HPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCY
GRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGL
PRIQELFEARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYT
APYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQK
VYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEAN
KKVLLEGNRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKG
KRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVS
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 chain6wvk Chain D Residue 2002 [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]
PDB6wvk Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD.
Resolution3.36 Å
Binding residue
(original residue number in PDB)		C818 C892 C899 C902
Binding residue
(residue number reindexed from 1)		C815 C889 C896 C899
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0046677 response to antibiotic
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6wvk, PDBe:6wvk, PDBj:6wvk
PDBsum6wvk
PubMed33339820
UniProtP37871|RPOC_BACSU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]