› 6qx2

X-ray diffraction
3.4Å resolution

3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA

Released:
DOI: 10.2210/pdb6qx2/pdb
PDB entry 6qx2 coloured by chain, front view.
PDB entry 6qx2 coloured by chain, side view.
PDB entry 6qx2 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-219020 (preferred)
Entry contents:
9 distinct polypeptide molecules
3 distinct DNA molecules
Macromolecules (12 distinct):
DNA gyrase subunit B Chains: B, S, b, s
Molecule details ›
Chains: B, S, b, s
Length: 186 amino acids
Theoretical weight: 20.85 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-638; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit A Chains: A, C, L, R, T, a, c, j, l, r, t
Molecule details ›
Chains: A, C, L, R, T, a, c, j, l, r, t
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 gyrase subunit B Chains: D, U, m
Molecule details ›
Chains: D, U, m
Length: 188 amino acids
Theoretical weight: 21.11 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-638; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit B Chain: K
Molecule details ›
Chain: K
Length: 187 amino acids
Theoretical weight: 21.01 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-639; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit A Chain: J
Molecule details ›
Chain: J
Length: 480 amino acids
Theoretical weight: 54.37 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 11-491; Coverage: 54%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA gyrase subunit B Chain: M
Molecule details ›
Chain: M
Length: 189 amino acids
Theoretical weight: 21.27 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-639; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit B Chain: d
Molecule details ›
Chain: d
Length: 181 amino acids
Theoretical weight: 20.36 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 586-637; Coverage: 28%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit B Chain: k
Molecule details ›
Chain: k
Length: 188 amino acids
Theoretical weight: 21.08 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 416-640; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA gyrase subunit B Chain: u
Molecule details ›
Chain: u
Length: 187 amino acids
Theoretical weight: 21.01 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: P0A0K8 (Residues: 417-543, 580-637; Coverage: 29%)
Gene name: gyrB
Sequence domains:
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chains: E, F, N, O, W, e, n, v, w
Molecule details ›
Chains: E, F, N, O, W, e, n, v, w
Length: 20 nucleotides
Theoretical weight: 6.15 KDa
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chains: V, o
Molecule details ›
Chains: V, o
Length: 19 nucleotides
Theoretical weight: 5.85 KDa
DNA (5'-D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') Chain: f
Molecule details ›
Chain: f
Length: 17 nucleotides
Theoretical weight: 5.2 KDa

Ligands and Environments

1 bound ligand:
Ligand JK8 12 x JK8
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I23
Spacegroup: P21
Unit cell:
a: 187.64Å b: 410.12Å c: 93.94Å
α: 90° β: 120.22° γ: 90°
R-values:
R R work R free
0.178 0.176 0.208
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

A 2.8 Å Structure of Zoliflodacin in a DNA Cleavage Complex with Staphylococcus aureus DNA Gyrase.
Morgan et al. (2023)
2 more

3 mentions without citation

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