Structure of PDB 6vvv Chain D Binding Site BS02

Receptor Information
>6vvv Chain D (length=1174) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIF
GPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVT
HIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLE
AEMAVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGE
REMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYF
TGAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAF
QQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNN
RLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSL
SDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELF
KPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAP
TLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQ
AEARILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAA
TKDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFE
NGWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAER
FPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEA
DAIERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIV
KSGATTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGPIRDAH
VETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVKVRSV
LTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQGGLPRV
QELFEARVPRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVYDKLS
KRQRLRVIGVLSDGDHVEVGDQLMEGAADPHEVLRVQGPREVQIHLVKEV
QEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDFLPGSLTERAEFAAGRPVL
MGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKL
IPAGTGISRYRNIQVQPTEEARAA
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 chain6vvv Chain D Residue 1410 [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]
PDB6vvv The antibiotic sorangicin A inhibits promoter DNA unwinding in a Mycobacterium tuberculosis rifampicin-resistant RNA polymerase.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		C60 C62 C75 C78
Binding residue
(residue number reindexed from 1)		C58 C60 C73 C76
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: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
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:6vvv, PDBe:6vvv, PDBj:6vvv
PDBsum6vvv
PubMed33199626
UniProtA0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]