› 1rfi

X-ray diffraction
2.2Å resolution

Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, pentapeptide KLNYK, and tetranucleotide AGTC

Released:
DOI: 10.2210/pdb1rfi/pdb
PDB entry 1rfi coloured by chain, front view.
PDB entry 1rfi coloured by chain, side view.
PDB entry 1rfi 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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114516 (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 Chains: C, E
Molecule details ›
Chains: C, E
Length: 5 amino acids
Theoretical weight: 667 Da
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*AP*GP*TP*C)-3' Chains: D, F
Molecule details ›
Chains: D, F
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.2
Spacegroup: P212121
Unit cell:
a: 49.82Å b: 104.832Å c: 193.539Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.188 0.227
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