› 5inq

X-ray diffraction
1.85Å resolution

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Ca2+ complex

Released:
DOI: 10.2210/pdb5inq/pdb
PDB entry 5inq coloured by chain, front view.
PDB entry 5inq coloured by chain, side view.
PDB entry 5inq 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
OpenAccess logo 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-118795 (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*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 54.702Å b: 67.504Å c: 167.529Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.159 0.158 0.195
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)