› 4gfn

X-ray diffraction
1.9Å resolution

Pyrrolopyrimidine inhibitors of dna gyrase b and topoisomerase iv, part i: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic

Released:
DOI: 10.2210/pdb4gfn/pdb
PDB entry 4gfn coloured by chain, front view.
PDB entry 4gfn coloured by chain, side view.
PDB entry 4gfn coloured by chain, top view.
Source organism: Enterococcus faecalis V583
Primary publication:
Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity.
Tari LW, Trzoss M, Bensen DC, Li X, Chen Z, Lam T, Zhang J, Creighton CJ, Cunningham ML, Kwan B, Stidham M, Shaw KJ, Lightstone FC, Wong SE, Nguyen TB, Nix J, Finn J
Bioorg Med Chem Lett 23 1529-36 (2013)
PMID: 23352267

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-182889 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit B Chain: A
Molecule details ›
Chain: A
Length: 215 amino acids
Theoretical weight: 23.84 KDa
Source organism: Enterococcus faecalis V583
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q839Z1 (Residues: 18-224; Coverage: 32%)
Gene names: EF_0005, gyrB
Sequence domains: Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
Structure domains: Histidine kinase-like ATPase, C-terminal domain

Ligands and Environments

2 bound ligands:
Ligand SUY 1 x SUY
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 4.2.2
Spacegroup: P212121
Unit cell:
a: 54.78Å b: 58.21Å c: 66.19Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.223 0.162 0.212
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Targeting DNA Replication and Repair for the Development of Novel Therapeutics against Tuberculosis.
Reiche et al. (2017)
4 more