› 4gz2

X-ray diffraction
1.85Å resolution

Mus Musculus Tdp2 excluded ssDNA complex

Released:
DOI: 10.2210/pdb4gz2/pdb
PDB entry 4gz2 coloured by chain, front view.
PDB entry 4gz2 coloured by chain, side view.
PDB entry 4gz2 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Schellenberg MJ, Appel CD, Adhikari S, Robertson PD, Ramsden DA, Williams RS
OpenAccess logo Nat Struct Mol Biol 19 1363-71 (2012)
PMID: 23104055

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-117569 (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: 255 amino acids
Theoretical weight: 28.78 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9JJX7 (Residues: 118-369; Coverage: 68%)
Gene names: Tdp2, Ttrap
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
DNA (5'-D(*CP*AP*TP*CP*CP*GP*AP*AP*TP*TP*CP*G)-3') Chains: C, D
Molecule details ›
Chains: C, D
Length: 12 nucleotides
Theoretical weight: 3.62 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand FMT 2 x FMT
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P21
Unit cell:
a: 60.483Å b: 42.972Å c: 107.951Å
α: 90° β: 95.89° γ: 90°
R-values:
R R work R free
0.208 0.205 0.245
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

11 review citations

Tyrosyl-DNA-phosphodiesterases (TDP1 and TDP2).
Pommier et al. (2014)
10 more

2 mentions without citation

Mechanism of repair of 5'-topoisomerase II-DNA adducts by mammalian tyrosyl-DNA phosphodiesterase 2.
Schellenberg et al. (2012)
1 more