› 5ctu

X-ray diffraction
1.45Å resolution

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment

Released:
DOI: 10.2210/pdb5ctu/pdb
PDB entry 5ctu coloured by chain, front view.
PDB entry 5ctu coloured by chain, side view.
PDB entry 5ctu coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Fragment-based discovery of DNA gyrase inhibitors targeting the ATPase subunit of GyrB.
Mesleh MF, Cross JB, Zhang J, Kahmann J, Andersen OA, Barker J, Cheng RK, Felicetti B, Wood M, Hadfield AT, Scheich C, Moy TI, Yang Q, Shotwell J, Nguyen K, Lippa B, Dolle R, Ryan MD
Bioorg Med Chem Lett 26 1314-8 (2016)
PMID: 26786695

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-140941 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chains: A, B
Molecule details ›
Chains: A, B
Length: 212 amino acids
Theoretical weight: 23.93 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A0K8 (Residues: 2-234; Coverage: 33%)
Gene name: gyrB
Sequence domains: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Structure domains: Histidine kinase-like ATPase, C-terminal domain

Ligands and Environments

4 bound ligands:
Ligand MPD 3 x MPD
Ligand CL 1 x CL
Ligand 54X 2 x 54X
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 142.66Å b: 55.65Å c: 51.14Å
α: 90° β: 101.01° γ: 90°
R-values:
R R work R free
0.178 0.176 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Recent progress in the discovery and development of DNA gyrase B inhibitors.
Barančoková et al. (2018)
8 other articles

3 mentions without citation

Photocatalytic and bactericidal properties and molecular docking analysis of TiO2 nanoparticles conjugated with Zr for environmental remediation.
Ikram et al. (2020)
2 more