PDBe 1de9

X-ray diffraction
3Å resolution



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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA-(apurinic or apyrimidinic site) lyase, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
  • Canonical: P27695 (Residues: 43-318; Coverage: 87%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
5'-d(*CP*TP*AP*C)-3' Chains: U, X
Molecule details ›
Chains: U, X
Length: 4 nucleotides
Theoretical weight: 1.15 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-d(P*(3DR)P*GP*AP*TP*C)-3' Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 5 nucleotides
Theoretical weight: 1.37 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' Chains: W, Z
Molecule details ›
Chains: W, Z
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: P212121
Unit cell:
a: 90.06Å b: 98.35Å c: 101.05Å
α: 90° β: 90° γ: 90°
R R work R free
0.183 0.183 0.274
Expression systems:
  • Escherichia coli
  • Not provided