› 5ink

X-ray diffraction
2.15Å resolution

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-abasic/THF-Mg2+ complex

Released:
DOI: 10.2210/pdb5ink/pdb
PDB entry 5ink coloured by chain, front view.
PDB entry 5ink coloured by chain, side view.
PDB entry 5ink coloured by chain, top view.
Source organisms:
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:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118791 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 distinct):
Tyrosyl-DNA phosphodiesterase 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 256 amino acids
Theoretical weight: 28.91 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
DNA (5'-D(P*(3DR)P*CP*GP*AP*AP*TP*TP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.61 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 54.615Å b: 67.662Å c: 166.745Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.165 0.165 0.201
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

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

1 mention without citation

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