› 5j3p

X-ray diffraction
3.1Å resolution

Crystal structure of the catalytic domain of human tyrosyl DNA phosphodiesterase 2

Released:
DOI: 10.2210/pdb5j3p/pdb
PDB entry 5j3p coloured by chain, front view.
PDB entry 5j3p coloured by chain, side view.
PDB entry 5j3p coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Hornyak P, Askwith T, Walker S, Komulainen E, Paradowski M, Pennicott LE, Bartlett EJ, Brissett NC, Raoof A, Watson M, Jordan AM, Ogilvie DJ, Ward SE, Atack JR, Pearl LH, Caldecott KW, Oliver AW
Biochem J 473 1869-79 (2016)
PMID: 27099339

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-131947 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosyl-DNA phosphodiesterase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 253 amino acids
Theoretical weight: 28.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95551 (Residues: 113-362; Coverage: 69%)
Gene names: AD-022, EAP2, TDP2, TTRAP
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P3121
Unit cell:
a: 92.545Å b: 92.545Å c: 119.075Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.258 0.256 0.291
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Recent developments in topoisomerase-targeted cancer chemotherapy.
Hevener et al. (2018)
3 more

2 mentions without citation

Mode of action of DNA-competitive small molecule inhibitors of tyrosyl DNA phosphodiesterase 2.
Hornyak et al. (2016)
1 more