› 5z9f

X-ray diffraction
1.76Å resolution

Bacterial GyrB ATPase domain in complex with a chemical fragment

Released:
DOI: 10.2210/pdb5z9f/pdb
PDB entry 5z9f coloured by chain, front view.
PDB entry 5z9f coloured by chain, side view.
PDB entry 5z9f coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Identification of an auxiliary druggable pocket in the DNA gyrase ATPase domain using fragment probes.
Huang X, Guo J, Liu Q, Gu Q, Xu J, Zhou H
Medchemcomm 9 1619-1629 (2018)
PMID: 30429968

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142496 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 207 amino acids
Theoretical weight: 22.71 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AES6 (Residues: 15-221; 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
Structure domains: Histidine kinase-like ATPase, C-terminal domain

Ligands and Environments

3 bound ligands:
Ligand PO4 4 x PO4
Ligand 0R0 2 x 0R0
Ligand AX7 1 x AX7
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 61.587Å b: 68.097Å c: 102.124Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.199 0.224
Expression system: Escherichia coli

Quick links

Citations

5 citation in other articles

CycA-Dependent Glycine Assimilation Is Connected to Novobiocin Susceptibility in Escherichia coli.
Shi et al. (2022)
4 more

2 mentions without citation

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