› 4gyz

X-ray diffraction
2.56Å resolution

Mus Musculus Tdp2 Bound to dAMP and Mg2+

Released:
DOI: 10.2210/pdb4gyz/pdb
PDB entry 4gyz coloured by chain, front view.
PDB entry 4gyz coloured by chain, side view.
PDB entry 4gyz coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS
Nat Struct Mol Biol 19 1363-71 (2012)
PMID: 23104055

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, C, D, E, F, G, H, I
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I
Length: 256 amino acids
Theoretical weight: 28.89 KDa
Source organism: Mus musculus
Expression system: bacterium 2b-G12
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

4 bound ligands:
Ligand D5M 6 x D5M
Ligand MG 9 x MG
Ligand CL 3 x CL
Ligand PO4 1 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 85.347Å b: 169.326Å c: 184.959Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.191 0.22
Expression system: bacterium 2b-G12

Quick links

Citations

11 review citations

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

4 mentions without citation

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism.
Cuskin et al. (2015)
3 more