› 2y3p

X-ray diffraction
2.62Å resolution

Crystal structure of N-terminal domain of GyrA with the antibiotic simocyclinone D8

Released:
DOI: 10.2210/pdb2y3p/pdb
PDB entry 2y3p coloured by chain, front view.
PDB entry 2y3p coloured by chain, side view.
PDB entry 2y3p coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.
Edwards MJ, Flatman RH, Mitchenall LA, Stevenson CE, Le TB, Clarke TA, McKay AR, Fiedler HP, Buttner MJ, Lawson DM, Maxwell A
Science 326 1415-8 (2009)
PMID: 19965760

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:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142495 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA gyrase subunit A Chains: A, B
Molecule details ›
Chains: A, B
Length: 522 amino acids
Theoretical weight: 58.62 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli
UniProt:
  • Canonical: P0AES5 (Residues: 2-523; Coverage: 60%)
Gene names: S2444, SF2311, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 4 x MG
Ligand SM8 2 x SM8
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: I212121
Unit cell:
a: 143.91Å b: 153.09Å c: 177.7Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.241
Expression system: Escherichia coli

Quick links

Citations

13 review citations

All tangled up: how cells direct, manage and exploit topoisomerase function.
Vos et al. (2011)
12 more

4 mentions without citation

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