Structure of PDB 8to1 Chain I Binding Site BS02

Receptor Information
>8to1 Chain I (length=1337) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEA
AFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLR
LVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHR
SPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRR
RKLPATIILRALNYTTEQILDLFFEKVIFEIKLQMELVPERLRGTASFDI
EANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDES
TGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDP
TNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKF
NRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRS
VGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEF
FGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHY
GRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHY
LSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDV
STQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGME
RAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTK
YTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFM
PWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIP
NVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAI
FGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQ
AKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDE
EKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLA
VKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPS
RMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADV
RQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLP
TSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVT
QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMY
KNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE
Ligand information
Ligand ID4QM
InChIInChI=1S/C24H42O3/c1-5-6-14(2)17-7-8-18-22-19(13-21(27)24(17,18)4)23(3)10-9-16(25)11-15(23)12-20(22)26/h14-22,25-27H,5-13H2,1-4H3/t14-,15+,16-,17-,18+,19+,20-,21+,22+,23+,24-/m1/s1
InChIKeyPFZUIDNKXWIWBG-YHEMGIGTSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCC[CH](C)[CH]1CC[CH]2[CH]3[CH](O)C[CH]4C[CH](O)CC[C]4(C)[CH]3C[CH](O)[C]12C
OpenEye OEToolkits 2.0.4CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C@H]3[C@H]2[C@@H](C[C@H]4[C@@]3(CC[C@H](C4)O)C)O)O)C
CACTVS 3.385CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3[C@H](O)C[C@@H]4C[C@H](O)CC[C@]4(C)[C@H]3C[C@H](O)[C@]12C
OpenEye OEToolkits 2.0.4CCCC(C)C1CCC2C1(C(CC3C2C(CC4C3(CCC(C4)O)C)O)O)C
FormulaC24 H42 O3
Name(3R,5S,7R,8R,9S,10S,12S,13R,14S,17R)-10,13-dimethyl-17-[(2R)-pentan-2-yl]-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthrene-3,7,12-triol
ChEMBL
DrugBank
ZINCZINC000118924531
PDB chain8to1 Chain I Residue 1402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8to1 Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		Q46 Y47 Y179 S398 V400 E458 E583 Y584
Binding residue
(residue number reindexed from 1)		Q45 Y46 Y178 S393 V395 E453 E578 Y579
Annotation score1
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: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:8to1, PDBe:8to1, PDBj:8to1
PDBsum8to1
PubMed38951624
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

[Back to BioLiP]