› 6qx1

X-ray diffraction
2.65Å resolution

2.7A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA.

Released:
DOI: 10.2210/pdb6qx1/pdb
PDB entry 6qx1 coloured by chain, front view.
PDB entry 6qx1 coloured by chain, side view.
PDB entry 6qx1 coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Structure-guided design of antibacterials that allosterically inhibit DNA gyrase.
Thalji RK, Raha K, Andreotti D, Checchia A, Cui H, Meneghelli G, Profeta R, Tonelli F, Tommasi S, Bakshi T, Donovan BT, Howells A, Jain S, Nixon C, Quinque G, McCloskey L, Bax BD, Neu M, Chan PF, Stavenger RA
Bioorg Med Chem Lett 29 1407-1412 (2019)
PMID: 30962087

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:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120510 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
DNA gyrase subunit B Chains: B, D
Molecule details ›
Chains: B, D
Length: 202 amino acids
Theoretical weight: 22.61 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 409-543; Coverage: 21%)
Gene name: gyrB
Sequence domains: Toprim domain
DNA gyrase subunit A Chains: A, C
Molecule details ›
Chains: A, C
Length: 490 amino acids
Theoretical weight: 55.54 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 20 nucleotides
Theoretical weight: 6.13 KDa

Ligands and Environments

5 bound ligands:
Ligand MN 2 x MN
Ligand JK8 2 x JK8
Ligand GOL 5 x GOL
Ligand GLY 1 x GLY
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P61
Unit cell:
a: 93.19Å b: 93.19Å c: 408.99Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.164 0.162 0.206
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

De novo design of type II topoisomerase inhibitors as potential antimicrobial agents targeting a novel binding region.
Orritt et al. (2022)
1 more

3 mentions without citation

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
2 more