› 6tyz

X-ray diffraction
1.51Å resolution

Structure of Ku80 von Willebrand domain complexed with APLF Ku Binding Motif

Released:
DOI: 10.2210/pdb6tyz/pdb
PDB entry 6tyz coloured by chain, front view.
PDB entry 6tyz coloured by chain, side view.
PDB entry 6tyz coloured by chain, top view.
Source organisms:
Primary publication:
Ligand binding characteristics of the Ku80 von Willebrand domain.
Kim K, Min J, Kirby TW, Gabel SA, Pedersen LC, London RE
DNA Repair (Amst) 85 102739 (2020)
PMID: 31733588

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-233041 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
X-ray repair cross-complementing protein 5 Chain: A
Molecule details ›
Chain: A
Length: 231 amino acids
Theoretical weight: 26.19 KDa
Source organism: Xenopus laevis
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6DDS9 (Residues: 1-242; Coverage: 29%)
Gene names: xrcc5, xrcc5.L
Sequence domains: Ku70/Ku80 N-terminal alpha/beta domain
Aprataxin and PNK-like factor Chain: B
Molecule details ›
Chain: B
Length: 16 amino acids
Theoretical weight: 1.97 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q8IW19 (Residues: 179-194; Coverage: 3%)
Gene names: APLF, C2orf13, PALF, XIP1

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 43.807Å b: 71.189Å c: 79.527Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.179 0.178 0.203
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

4 review citations

Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway.
Stinson et al. (2021)
3 more

1 mention without citation

Ligand binding characteristics of the Ku80 von Willebrand domain.
Kim et al. (2020)