Structure of PDB 6gfw Chain D Binding Site BS01

Receptor Information
>6gfw Chain D (length=1345) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPER
DGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMG
HIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTN
LERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLRE
ELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV
PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAV
DALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRS
VITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVER
EEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV
CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPS
QDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRIT
EYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISK
MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEI
ISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT
ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGS
IIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV
AQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGT
ADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDL
ARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVK
NKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVL
AKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQSSLV
VLDSAERRPALKIVDAQGNDVAQYFLPGKAIVQLEDGVQISSGDTLARIP
QDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVD
GSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTR
YIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVE
YSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRV
LTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAG
Ligand information
>6gfw Chain F (length=50) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
tgcgcaacagcatgcgcgcccagggctgatcgtgcaaaagtcgtgccagc
Receptor-Ligand Complex Structure
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PDB6gfw Structures of Bacterial RNA Polymerase Complexes Reveal the Mechanism of DNA Loading and Transcription Initiation.
Resolution3.7 Å
Binding residue
(original residue number in PDB)		Y46 E211 R270 S319 A791 Y795 E1327
Binding residue
(residue number reindexed from 1)		Y43 E208 R267 S316 A788 Y792 E1296
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6gfw, PDBe:6gfw, PDBj:6gfw
PDBsum6gfw
PubMed29932903
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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