› 6djg

X-ray diffraction
1.88Å resolution

Crystal structure of Tdp1 catalytic domain in complex with compound XZ503

Released:
DOI: 10.2210/pdb6djg/pdb
PDB entry 6djg coloured by chain, front view.
PDB entry 6djg coloured by chain, side view.
PDB entry 6djg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening.
Lountos GT, Zhao XZ, Kiselev E, Tropea JE, Needle D, Pommier Y, Burke TR, Waugh DS
Nucleic Acids Res 47 10134-10150 (2019)
PMID: 31199869

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence 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: 461 amino acids
Theoretical weight: 52.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NUW8 (Residues: 148-608; Coverage: 76%)
Gene name: TDP1
Sequence domains: Tyrosyl-DNA phosphodiesterase
Structure domains: Endonuclease Chain A

Ligands and Environments

2 bound ligands:
Ligand EDO 2 x EDO
Ligand GNJ 2 x GNJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 49.538Å b: 105.316Å c: 193.736Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.183 0.182 0.225
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Excision repair of topoisomerase DNA-protein crosslinks (TOP-DPC).
Sun et al. (2020)
17 other articles