› 5ino

X-ray diffraction
3.2Å resolution

Human Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex

Released:
DOI: 10.2210/pdb5ino/pdb
PDB entry 5ino coloured by chain, front view.
PDB entry 5ino coloured by chain, side view.
PDB entry 5ino coloured by chain, top view.
Source organism: Homo sapiens
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-118793 (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: 258 amino acids
Theoretical weight: 29.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O95551 (Residues: 108-362; Coverage: 70%)
Gene names: AD-022, EAP2, 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

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P31
Unit cell:
a: 69.663Å b: 69.663Å c: 120.677Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.216 0.214 0.264
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

3 mentions without citation

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