Structure of PDB 8pdy Chain I Binding Site BS02

Receptor Information
>8pdy Chain I (length=1323) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLE
AAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKL
RLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLH
RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDR
RRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGET
ASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISET
LRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV
GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGN
RRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISA
AVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDV
HPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV
DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLV
GTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDI
YNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM
RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEI
TADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGEDVKDSSLR
VPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEA
GLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYD
ELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGR
HGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM
AAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEV
MRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGE
QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQR
FGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGM
PESFNVLLKEIRSLGINIELEDE
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)		R151 W183 D199 R200 R201 R371 R394 I445 R470 R473 L538 R542 V547
Binding residue
(residue number reindexed from 1)		R151 W183 D199 R200 R201 R371 R394 I445 R470 R473 L538 R542 V547
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
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:8pdy, PDBe:8pdy, PDBj:8pdy
PDBsum8pdy
PubMed38589445
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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