› 5npk

X-ray diffraction
1.98Å resolution

1.98A STRUCTURE OF THIOPHENE1 WITH S.AUREUS DNA GYRASE AND DNA

Released:
DOI: 10.2210/pdb5npk/pdb
PDB entry 5npk coloured by chain, front view.
PDB entry 5npk coloured by chain, side view.
PDB entry 5npk coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Primary publication:
Thiophene antibacterials that allosterically stabilize DNA-cleavage complexes with DNA gyrase.
Chan PF, Germe T, Bax BD, Huang J, Thalji RK, Bacqué E, Checchia A, Chen D, Cui H, Ding X, Ingraham K, McCloskey L, Raha K, Srikannathasan V, Maxwell A, Stavenger RA
Proc Natl Acad Sci U S A 114 E4492-E4500 (2017)
PMID: 28507124

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119069 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
DNA gyrase subunit A; DNA gyrase subunit B Chains: B, D, b, d
Molecule details ›
Chains: B, D, b, d
Length: 692 amino acids
Theoretical weight: 78.11 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 409-543, 580-642; Coverage: 31%)
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0005, SA0006, gyrA, gyrB
Sequence domains:
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, e, f
Molecule details ›
Chains: E, F, e, f
Length: 20 nucleotides
Theoretical weight: 6.13 KDa

Ligands and Environments

7 bound ligands:
Ligand MN 5 x MN
Ligand 94H 6 x 94H
Ligand GOL 13 x GOL
Ligand CL 1 x CL
Ligand SO4 1 x SO4
Ligand NA 1 x NA
Ligand 9JN 2 x 9JN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P21
Unit cell:
a: 89.442Å b: 120.68Å c: 168.899Å
α: 90° β: 90.05° γ: 90°
R-values:
R R work R free
0.155 0.154 0.183
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance.
Bush et al. (2020)
2 more

5 mentions without citation

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