› 3m6z

X-ray diffraction
1.4Å resolution

Crystal structure of an N-terminal 44 kDa fragment of topoisomerase V in the presence of guanidium hydrochloride

Released:
DOI: 10.2210/pdb3m6z/pdb
PDB entry 3m6z coloured by chain, front view.
PDB entry 3m6z coloured by chain, side view.
PDB entry 3m6z coloured by chain, top view.
Source organism: Methanopyrus kandleri AV19
Primary publication:
Structures of minimal catalytic fragments of topoisomerase V reveals conformational changes relevant for DNA binding.
Rajan R, Taneja B, Mondragón A
Structure 18 829-38 (2010)
PMID: 20637419

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188858 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Helix-hairpin-helix DNA-binding motif class 1 domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 380 amino acids
Theoretical weight: 44.23 KDa
Source organism: Methanopyrus kandleri AV19
Expression system: Escherichia coli
UniProt:
  • Canonical: Q977W1 (Residues: 1-380; Coverage: 39%)
Gene names: HA336_03250, top5
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand PO4 7 x PO4
Ligand MG 3 x MG
Ligand CL 2 x CL
Ligand GAI 3 x GAI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-G, APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 63.64Å b: 80.11Å c: 137.22Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.165 0.184
Expression system: Escherichia coli

Quick links

Citations

1 review citation

DNA topoisomerases as molecular targets for anticancer drugs.
Buzun et al. (2020)
4 other articles

2 mentions without citation

Identification of one of the apurinic/apyrimidinic lyase active sites of topoisomerase V by structural and functional studies.
Rajan et al. (2013)
1 more