Structure of PDB 6p1k Chain J Binding Site BS01

Receptor Information
>6p1k Chain J (length=1325) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL
ELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLN
RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTL
EAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEG
MVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTV
GRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQI
MYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVT
AGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYM
MADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFI
STHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTP
VIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEE
NSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIG
EPGTQLTSSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGR
TKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM
IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLI
PGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQGLPRVADLFEARRP
KEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE
GERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKIND
KHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGA
TYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKEN
VIVGRLIPAGTGYAYHQDRMRRRAA
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 chain6p1k Chain J Residue 1501 [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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PDB6p1k E. coliTraR allosterically regulates transcription initiation by altering RNA polymerase conformation.
Resolution4.05 Å
Binding residue
(original residue number in PDB)		D462 D464
Binding residue
(residue number reindexed from 1)		D438 D440
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6p1k, PDBe:6p1k, PDBj:6p1k
PDBsum6p1k
PubMed31841111
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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