Structure of PDB 4zh3 Chain C Binding Site BS01

Receptor Information

>4zh3 Chain C (length=1340) Species: 83333 (Escherichia coli K-12)

YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAA
FRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRL
VIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRS
PGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR
KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETAS
FDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYI
DESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLR
VDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR
MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRR
IRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAV
KEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHP
THYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE
IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDY
MDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGT
GMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYN
LTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV
AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA
DIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLL
RAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQ
LKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL
TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKV
YLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLG
VPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLG
ADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG
DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYS
LVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRT
KMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

Ligand information

• Ligand ID: 4OD
• InChI: InChI=1S/C14H9BrF4N2O/c15-9-2-1-3-10(7-9)20-13(21-22)8-4-5-12(16)11(6-8)14(17,18)19/h1-7,22H,(H,20,21)
• InChIKey: HYMULNGSTZFRLI-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.9.2: c1cc(cc(c1)Br)N=C(c2ccc(c(c2)C(F)(F)F)F)NO
  OpenEye OEToolkits 1.9.2: c1cc(cc(c1)Br)/N=C(\c2ccc(c(c2)C(F)(F)F)F)/NO
  ACDLabs 12.01: FC(c1c(ccc(c1)/C(NO)=N\c2cc(Br)ccc2)F)(F)F
  CACTVS 3.385: ONC(=Nc1cccc(Br)c1)c2ccc(F)c(c2)C(F)(F)F
• Formula: C14 H9 Br F4 N2 O
• Name: N'-(3-bromophenyl)-4-fluoro-N-hydroxy-3-(trifluoromethyl)benzenecarboximidamide
• ZINC: ZINC000263620537
• PDB chain: 4zh3 Chain D Residue 1504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4zh3 Structural Basis of Transcription Inhibition by CBR Hydroxamidines and CBR Pyrazoles.
• Resolution: 4.082 Å
• Binding residue (original residue number in PDB): P552 Y555 R637 S642
• Binding residue (residue number reindexed from 1): P550 Y553 R635 S640
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.40,IC50=40uM

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

External links

• PDB: RCSB:4zh3, PDBe:4zh3, PDBj:4zh3
• PDBsum: 4zh3
• PubMed: 26190576
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)