Structure of PDB 4ylp Chain I Binding Site BS02

Receptor Information
>4ylp Chain I (length=1341) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEA
AFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLR
LVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHR
SPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRR
RKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETA
SFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDY
IDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL
RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVG
RMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNR
RIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA
VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVH
PTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTD
EIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD
YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVG
TGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIY
NLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR
VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEIT
ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKL
LRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEM
QLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELG
LTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVK
VYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPL
GVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDL
GADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKL
GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSY
SLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGR
TKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
>4ylp Chain 5 (length=49) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
gccgcgtcagactcgtaggattatagcatacgtgaggtggatgtcaagt
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4ylp Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.
Resolution5.5 Å
Binding residue
(original residue number in PDB)		R202 K496 A500 F514 G1261 K1262 R1269 M1273
Binding residue
(residue number reindexed from 1)		R201 K495 A499 F513 G1260 K1261 R1268 M1272
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ylp, PDBe:4ylp, PDBj:4ylp
PDBsum4ylp
PubMed25866247
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

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