Structure of PDB 4mey Chain D Binding Site BS02

Receptor Information
>4mey Chain D (length=1147) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFC
ARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELA
SPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQ
ILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNET
NSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGG
RFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLD
NGRRGRAITGSNKRPLKSLADMIKKRVDYSGRSVITVGPYLRLHQCGLPK
KMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHP
VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHV
PLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNA
KGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLK
DTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIF
ADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQS
GLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFN
SIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVL
QYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGI
MMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCD
LLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAA
QSIGEPGTQGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVI
TPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVH
AVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEG
EQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQE
TTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRA
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 chain4mey Chain D Residue 2001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4mey Transcription inhibition by the depsipeptide antibiotic salinamide A.
Resolution3.948 Å
Binding residue
(original residue number in PDB)		C70 C85 C88
Binding residue
(residue number reindexed from 1)		C62 C77 C80
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:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4mey, PDBe:4mey, PDBj:4mey
PDBsum4mey
PubMed24843001
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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