Structure of PDB 5z4h Chain B Binding Site BS02

Receptor Information

>5z4h Chain B (length=190) Species: 83333 (Escherichia coli K-12)

LDAVRKRPGMYIGDTDDGTGLHHMVFEVVDNAIDEALAGHCKEIIVTIHA
DNSVSVQDDGRGIPTGIHPEEGVSAAEVIMTVLHAGVGVSVVNALSQKLE
LVIQREGKIHRQIYEHGVPQAPLAVTGETEKTGTMVRFWPSLETFTNVTE
FEYEILAKRLRELSFLNSGVSIRLRDKRDGKEDHFHYEGG

Ligand information

• Ligand ID: A8K
• InChI: InChI=1S/C12H10O2S/c13-9-1-5-11(6-2-9)15-12-7-3-10(14)4-8-12/h1-8,13-14H
• InChIKey: VWGKEVWFBOUAND-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Oc1ccc(Sc2ccc(O)cc2)cc1
  OpenEye OEToolkits 2.0.6: c1cc(ccc1O)Sc2ccc(cc2)O
• Formula: C12 H10 O2 S
• Name: 4-(4-hydroxyphenyl)sulfanylphenol
• ChEMBL: CHEMBL3183502
• ZINC: ZINC000000136154
• PDB chain: 5z4h Chain B Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5z4h Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): V43 N46 A47 Q72 D73 I78 A91 I94 M95 V120 T165 V167
• Binding residue (residue number reindexed from 1): V28 N31 A32 Q57 D58 I63 A76 I79 M80 V89 T134 V136
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006265 DNA topological change

External links

• PDB: RCSB:5z4h, PDBe:5z4h, PDBj:5z4h
• PDBsum: 5z4h
• PubMed: 30429968
• UniProt: P0AES6|GYRB_ECOLI DNA gyrase subunit B (Gene Name=gyrB)