› 5inm

X-ray diffraction
2.4Å resolution

Mouse Tdp2 protein, apo state with variable DNA-binding grasp conformations

Released:
DOI: 10.2210/pdb5inm/pdb
PDB entry 5inm coloured by chain, front view.
PDB entry 5inm coloured by chain, side view.
PDB entry 5inm coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
Schellenberg MJ, Perera L, Strom CN, Waters CA, Monian B, Appel CD, Vilas CK, Williams JG, Ramsden DA, Williams RS
Nucleic Acids Res 44 3829-44 (2016)
PMID: 27060144

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
Molecule details ›
Chains: A, B, C, D, E
Length: 256 amino acids
Theoretical weight: 28.91 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
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

3 bound ligands:
Ligand MG 4 x MG
Ligand GOL 1 x GOL
Ligand SO4 3 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 95.851Å b: 113.445Å c: 114.959Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.179 0.23
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC).
Sun et al. (2020)
4 more

2 mentions without citation

Reversal of DNA damage induced Topoisomerase 2 DNA-protein crosslinks by Tdp2.
Schellenberg et al. (2016)
1 more