› 1mu9

X-ray diffraction
2.05Å resolution

Crystal Structure of a Human Tyrosyl-DNA Phosphodiesterase (Tdp1)-Vanadate Complex

Released:
DOI: 10.2210/pdb1mu9/pdb
PDB entry 1mu9 coloured by chain, front view.
PDB entry 1mu9 coloured by chain, side view.
PDB entry 1mu9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Insights into substrate binding and catalytic mechanism of human tyrosyl-DNA phosphodiesterase (Tdp1) from vanadate and tungstate-inhibited structures.
Davies DR, Interthal H, Champoux JJ, Hol WG
J Mol Biol 324 917-32 (2002)
PMID: 12470949

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192623 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
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

Ligands and Environments

2 bound ligands:
Ligand VO4 2 x VO4
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P212121
Unit cell:
a: 50.028Å b: 104.98Å c: 194.297Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.199 0.214
Expression system: Escherichia coli BL21

Quick links

Citations

12 review citations

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

1 mention without citation

Structure Modeling of Human Tyrosyl-DNA Phosphodiesterase 1 and Screening for Its Inhibitors.
Gushchina et al. (2017)