› 5npp

X-ray diffraction
2.22Å resolution

2.22A STRUCTURE OF THIOPHENE2 AND GSK945237 WITH S.AUREUS DNA GYRASE AND DNA

Released:
DOI: 10.2210/pdb5npp/pdb
PDB entry 5npp coloured by chain, front view.
PDB entry 5npp coloured by chain, side view.
PDB entry 5npp 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 hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119070 (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: 78.13 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
Molecule details ›
Chains: E, F
Length: 8 nucleotides
Theoretical weight: 2.45 KDa
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: A, C
Molecule details ›
Chains: A, C
Length: 12 nucleotides
Theoretical weight: 3.64 KDa

Ligands and Environments

6 bound ligands:
Ligand MN 2 x MN
Ligand 94K 2 x 94K
Ligand GOL 9 x GOL
Ligand NA 1 x NA
Ligand DMS 1 x DMS
Ligand 6EJ 1 x 6EJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P61
Unit cell:
a: 92.85Å b: 92.85Å c: 409.98Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.182 0.227
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Topoisomerases as anticancer targets.
Delgado et al. (2018)
5 more

7 mentions without citation

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