› 5j42

X-ray diffraction
1.7Å resolution

Crystal structure of m2hTDP2-CAT in complex with a small molecule inhibitor

Released:
DOI: 10.2210/pdb5j42/pdb
PDB entry 5j42 coloured by chain, front view.
PDB entry 5j42 coloured by chain, side view.
PDB entry 5j42 coloured by chain, top view.
Source organism: Mus musculus
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-191622 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosyl-DNA phosphodiesterase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 256 amino acids
Theoretical weight: 28.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-370; Coverage: 68%)
Gene names: Tdp2, Ttrap
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

5 bound ligands:
Ligand 6FV 2 x 6FV
Ligand TLA 6 x TLA
Ligand GOL 2 x GOL
Ligand EDO 2 x EDO
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 61.054Å b: 42.872Å c: 109.054Å
α: 90° β: 94.05° γ: 90°
R-values:
R R work R free
0.162 0.16 0.197
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

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

3 mentions without citation

Molecular mechanisms of topoisomerase 2 DNA-protein crosslink resolution.
Riccio et al. (2020)
2 more