› 7dqw

X-ray diffraction
1.88Å resolution

E. coli GyrB ATPase domain in complex with 4-chlorophenol

Released:
DOI: 10.2210/pdb7dqw/pdb
PDB entry 7dqw coloured by chain, front view.
PDB entry 7dqw coloured by chain, side view.
PDB entry 7dqw coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Identification of new building blocks by fragment screening for discovering GyrB inhibitors.
Yu Y, Guo J, Cai Z, Ju Y, Xu J, Gu Q, Zhou H
Bioorg Chem 114 105040 (2021)
PMID: 34098257

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142497 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 206 amino acids
Theoretical weight: 22.65 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0AES6 (Residues: 16-221; Coverage: 26%)
Gene names: JW5625, acrB, b3699, cou, gyrB, himB, hisU, nalC, parA, pcbA
Sequence domains: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

Ligands and Environments

3 bound ligands:
Ligand AX7 1 x AX7
Ligand 4CH 2 x 4CH
Ligand PO4 3 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 61.666Å b: 67.492Å c: 103.214Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.246 0.245 0.263
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 citation in other articles

Pharmacophore-Based Virtual Screening and Molecular Dynamics Simulation for Identification of a Novel DNA Gyrase B Inhibitor with Benzoxazine Acetamide Scaffold.
Elseginy et al. (2022)
1 more

1 mention without citation

Developments in Non-Intercalating Bacterial Topoisomerase Inhibitors: Allosteric and ATPase Inhibitors of DNA Gyrase and Topoisomerase IV.
Grossman et al. (2023)