› 1rh0

X-ray diffraction
2.3Å resolution

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT

Released:
DOI: 10.2210/pdb1rh0/pdb
PDB entry 1rh0 coloured by chain, front view.
PDB entry 1rh0 coloured by chain, side view.
PDB entry 1rh0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Explorations of peptide and oligonucleotide binding sites of tyrosyl-DNA phosphodiesterase using vanadate complexes.
Davies DR, Interthal H, Champoux JJ, Hol WG
J Med Chem 47 829-37 (2004)
PMID: 14761185

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114521 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct DNA molecule
Macromolecules (2 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
5'-D(*GP*TP*T)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 3 nucleotides
Theoretical weight: 893 Da
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand VO4 2 x VO4
Ligand SPM 1 x SPM
Ligand OTS 2 x OTS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 49.692Å b: 104.75Å c: 194.033Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.188 0.235
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

11 review citations

Nucleases: diversity of structure, function and mechanism.
Yang W. (2011)
10 more

2 mentions without citation

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