Structure of PDB 8pdy Chain J Binding Site BS03

Receptor Information
>8pdy Chain J (length=1355) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIF
GPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTA
HIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTE
EQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSET
KRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFAT
SDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRR
GRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLR
LHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL
DEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFD
GDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGE
LVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRIL
GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVA
EIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQ
EEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITAN
FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED
DCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNT
LLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG
EAIGVIAAQSIGEPGTQLTMRTFHAAAESSIQVKNKGSIKLSNVKSVVNS
SGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVAN
WDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTA
GGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGD
TLARIPQESKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGK
RRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILR
LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSS
DFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISA
ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRR
RAAGE
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8pdy Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S210 E211 T212 L255 F260 T262 K334 R346 T790 A791 G794 Q1326 E1327 R1330
Binding residue
(residue number reindexed from 1)		S198 E199 T200 L243 F248 T250 K322 R334 T778 A779 G782 Q1304 E1305 R1308
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
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Biological Process
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Cellular Component
External links
PDB RCSB:8pdy, PDBe:8pdy, PDBj:8pdy
PDBsum8pdy
PubMed38589445
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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