Structure of PDB 6z11 Chain D Binding Site BS03

Receptor Information
>6z11 Chain D (length=1254) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFG
PTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTH
IWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEA
EMAVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGER
EMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYFT
GAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQ
SPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRL
IDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLK
GKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVM
KRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRL
GIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARI
LMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKDAP
EQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFENGWKP
GDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPMIV
VAQTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEADAIER
KYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKSGAT
GNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGARK
GLADTALRTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGPDG
TLIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGIT
TVKVRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGT
QLTMRTFHVGGLPRVQELFEARVPRNKAPIADVAGRVRLEESDKFFKITI
VPDDGGEEVVYDKLSKRQRLRVITHEEGVLSDGDHVEVGDQLMEGAADPH
EVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIID
SGSTEFLPGSLTERAEFEAENRRVGRPVLMGITKASLATDSWLSAASFQE
TTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEA
RAAA
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6z11 Chain D Residue 2003 [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]
PDB6z11 HelD, a helicase-like protein from gram-positive bacteria in complex with RNA polymerase
Resolution3.36 Å
Binding residue
(original residue number in PDB)		D535 D537 D539
Binding residue
(residue number reindexed from 1)		D528 D530 D532
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:6z11, PDBe:6z11, PDBj:6z11
PDBsum6z11
PubMed
UniProtA0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]