1de8

X-ray diffraction
2.95Å resolution

HUMAN APURINIC/APYRIMIDINIC ENDONUCLEASE-1 (APE1) BOUND TO ABASIC DNA

Released:

Function and Biology Details

Reaction catalysed:
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-113674 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1, 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
UniProt:
  • 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
DNA (5'-D(*GP*CP*TP*AP*CP*(3DR)P*GP*AP*TP*CP*G)-3') Chains: U, X
Molecule details ›
Chains: U, X
Length: 11 nucleotides
Theoretical weight: 3.23 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA (5'-D(*CP*GP*AP*TP*CP*GP*GP*TP*AP*GP*C)-3') Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 11 nucleotides
Theoretical weight: 3.37 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL9-1
Spacegroup: I41
Unit cell:
a: 122.85Å b: 122.85Å c: 107.07Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.312
Expression systems:
  • Escherichia coli
  • Not provided