Structure of PDB 8upr Chain AE Binding Site BS03

Receptor Information
>8upr Chain AE (length=1337) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGP
VKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHI
WFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQ
YLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGR
AITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLH
QCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD
QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT
RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELV
AKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI
QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEE
KQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFR
EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL
HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEA
IGVIAAQSIGEPGTQLTMRSSIQVKNKGSIKLSNVKSVVNSSGKLVITSR
NTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVI
TEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPAL
KIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQTG
GLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPY
EEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNE
VQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVK
IANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAA
VAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRR
Ligand information
>8upr Chain 7 (length=38) [Search RNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
auguuuuuuuuuuuuuuuuuuuuugauuuggugagagg
......................................
Receptor-Ligand Complex Structure
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PDB8upr Escherichia coli transcription-translation coupled complex class A (TTC-A) containing RfaH bound to ops signal, mRNA with a 21 nt long spacer, and fMet-tRNAs in E-site and P-site of the ribosome
Resolution5.3 Å
Binding residue
(original residue number in PDB)		R322 I394 K395 K398 D464
Binding residue
(residue number reindexed from 1)		R308 I380 K381 K384 D450
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:8upr, PDBe:8upr, PDBj:8upr
PDBsum8upr
PubMed39117885
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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