PDBe 3u8u

X-ray diffraction
2.15Å resolution

Crystal structure of Human Apurinic/Apyridinimic Endonuclease, Ape1 in a new crystal form

Source organism: Homo sapiens
Entry authors: Agarwal R, Naidu MD

Function and Biology Details

Reaction catalysed:
The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
DNA-(apurinic or apyrimidinic site) lyase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 318 amino acids
Theoretical weight: 35.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: P27695 (Residues: 1-318; Coverage: 100%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P21
Unit cell:
a: 95.84Å b: 97.284Å c: 132.15Å
α: 90° β: 90.91° γ: 90°
R R work R free
0.2 0.198 0.243
Expression system: Escherichia coli