› 5ht2

X-ray diffraction
1.43Å resolution

Mouse Tdp2 reaction product (5'-phosphorylated DNA)-Mg2+ complex with 1-N6-etheno-adenine

Released:
DOI: 10.2210/pdb5ht2/pdb
PDB entry 5ht2 coloured by chain, front view.
PDB entry 5ht2 coloured by chain, side view.
PDB entry 5ht2 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-118768 (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
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-370; Coverage: 68%)
Gene names: Tdp2, Ttrap
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA Chains: C, D
Molecule details ›
Chains: C, D
Length: 9 nucleotides
Theoretical weight: 2.76 KDa
Source organism: Escherichia coli
Expression system: Escherichia coli BL21

Ligands and Environments

3 bound ligands:
Ligand MG 3 x MG
Ligand EPE 1 x EPE
Ligand PEG 1 x PEG
1 modified residue:
Ligand EDA 2 x EDA

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 54.884Å b: 68.604Å c: 167.247Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.118 0.116 0.15
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21

Quick links

Citations

5 review citations

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

15 mentions without citation

Antidepressant-associated sexual dysfunction: impact, effects, and treatment.
Higgins et al. (2010)
14 more