› 4fva

X-ray diffraction
2.07Å resolution

Crystal structure of truncated Caenorhabditis elegans TDP2

Released:
DOI: 10.2210/pdb4fva/pdb
PDB entry 4fva coloured by chain, front view.
PDB entry 4fva coloured by chain, side view.
PDB entry 4fva coloured by chain, top view.
Source organism: Caenorhabditis elegans
Primary publication:
Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Shi K, Kurahashi K, Gao R, Tsutakawa SE, Tainer JA, Pommier Y, Aihara H
OpenAccess logo Nat Struct Mol Biol 19 1372-7 (2012)
PMID: 23104058

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-195048 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
5'-tyrosyl-DNA phosphodiesterase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 256 amino acids
Theoretical weight: 29.28 KDa
Source organism: Caenorhabditis elegans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9XWG3 (Residues: 107-362; Coverage: 71%)
Gene name: Y63D3A.4
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

3 bound ligands:
Ligand EDO 17 x EDO
Ligand MG 4 x MG
Ligand MLI 5 x MLI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P21
Unit cell:
a: 52.6Å b: 104.4Å c: 84.7Å
α: 90° β: 90.98° γ: 90°
R-values:
R R work R free
0.161 0.159 0.211
Expression system: Escherichia coli

Quick links

Citations

11 review citations

Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2).
Pommier et al. (2014)
10 more

3 mentions without citation

Structural basis for recognition of 5'-phosphotyrosine adducts by Tdp2.
Shi et al. (2012)
2 more