› 1nop

X-ray diffraction
2.3Å resolution

Crystal structure of human tyrosyl-DNA phosphodiesterase (Tdp1) in complex with vanadate, DNA and a human topoisomerase I-derived peptide

Released:
DOI: 10.2210/pdb1nop/pdb
PDB entry 1nop coloured by chain, front view.
PDB entry 1nop coloured by chain, side view.
PDB entry 1nop coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of a transition state mimic for Tdp1 assembled from vanadate, DNA, and a topoisomerase I-derived peptide.
Davies DR, Interthal H, Champoux JJ, Hol WG
Chem Biol 10 139-47 (2003)
PMID: 12618186

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:
Structure domain:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-114270 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
Tyrosyl-DNA phosphodiesterase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 485 amino acids
Theoretical weight: 54.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9NUW8 (Residues: 149-608; Coverage: 76%)
Gene name: TDP1
Sequence domains: Tyrosyl-DNA phosphodiesterase
Structure domains: Endonuclease Chain A
topoisomerase I-derived peptide Chain: C
Molecule details ›
Chain: C
Length: 8 amino acids
Theoretical weight: 1.02 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*GP*AP*GP*TP*T)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 6 nucleotides
Theoretical weight: 1.85 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand VO4 2 x VO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P212121
Unit cell:
a: 49.803Å b: 104.719Å c: 193.924Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.252
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

13 review citations

Drugging topoisomerases: lessons and challenges.
Pommier Y. (2013)
12 more

30 mentions without citation

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