› 6z1a

X-ray diffraction
2.3Å resolution

Ternary complex of Staphylococcus aureus DNA gyrase with AMK12 and DNA

Released:
DOI: 10.2210/pdb6z1a/pdb
PDB entry 6z1a coloured by chain, front view.
PDB entry 6z1a coloured by chain, side view.
PDB entry 6z1a coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds.
Kolarič A, Germe T, Hrast M, Stevenson CEM, Lawson DM, Burton NP, Vörös J, Maxwell A, Minovski N, Anderluh M
Nat Commun 12 150 (2021)
PMID: 33420011

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-121002 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA gyrase subunit A; DNA gyrase subunit B Chains: B, D
Molecule details ›
Chains: B, D
Length: 692 amino acids
Theoretical weight: 78.08 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P0A0K8 (Residues: 409-644; Coverage: 31%)
  • Canonical: P20831 (Residues: 2-491; Coverage: 55%)
Gene names: gyrA, gyrB
Sequence domains:
DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*G)-3') Chains: E, F
Molecule details ›
Chains: E, F
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
DNA (5'-D(P*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') Chains: G, H
Molecule details ›
Chains: G, H
Length: 12 nucleotides
Theoretical weight: 3.64 KDa

Ligands and Environments

5 bound ligands:
Ligand EPE 2 x EPE
Ligand MN 4 x MN
Ligand DMS 3 x DMS
Ligand CL 1 x CL
Ligand Q52 1 x Q52
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P61
Unit cell:
a: 92.592Å b: 92.592Å c: 405.464Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.181 0.179 0.217
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Towards Conformation-Sensitive Inhibition of Gyrase: Implications of Mechanistic Insight for the Identification and Improvement of Inhibitors.
Klostermeier D. (2021)
3 other articles

6 mentions without citation

The Structural Features of Novel Bacterial Topoisomerase Inhibitors That Define Their Activity on Topoisomerase IV.
Kokot et al. (2022)
5 more