Structure of PDB 3iyd Chain C Binding Site BS02

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 J (length=98) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
cttgttatccgctcacaattccacactaattacgagccggaagcataaag
tgtaaagccttttttgcctaaaatgtgatctagatcacatttattgcg
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)		Q1268 R1269 E1272
Binding residue
(residue number reindexed from 1)		Q1015 R1016 E1019
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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