Structure of PDB 3iyd Chain C Binding Site BS01

Receptor Information
>3iyd Chain C (length=1089) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPI
QSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREA
PEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS
DKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATII
LRALNYTTEQILDLFFEKVDLLAKLSQSGHKRIETLFTNDLDHGPYISET
LRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV
GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGN
RRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISA
AVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDV
HPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV
DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLV
GTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDI
YNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM
RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEI
TADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEK
LLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDLAPGVLKI
VKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLN
PLGVPSRMNIGQILETHLGMAAKGIGMPIATPVFDGAKEAEIKELLKLGD
LPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSL
VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTK
MYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
>3iyd Chain I (length=98) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cgcaataaatgtgatctagatcacattttaggcaaaaaaggctttacact
ttatgcttccggctcgtataatcgcaccttatgtgagcggataacaag
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB3iyd Three-dimensional EM structure of an intact activator-dependent transcription initiation complex
Resolution19.8 Å
Binding residue
(original residue number in PDB)		Y179 R180 W183 R200 F389 F390 N462 V466 G536 G537
Binding residue
(residue number reindexed from 1)		Y170 R171 W174 R191 F289 F290 N362 V366 G436 G437
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3iyd, PDBe:3iyd, PDBj:3iyd
PDBsum3iyd
PubMed19903881
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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