› 9dp3

X-ray diffraction
2.1Å resolution

APE1 N174D Product Complex with Abasic DNA

Released:
DOI: 10.2210/pdb9dp3/pdb
PDB entry 9dp3 coloured by chain, front view.
PDB entry 9dp3 coloured by chain, side view.
PDB entry 9dp3 coloured by chain, top view.
Source organisms:
Entry authors: Hoitsma NM, DeHart KD, Freudenthal BD

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero tetramer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-271059 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA repair nuclease/redox regulator APEX1, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.16 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
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') Chain: E
Molecule details ›
Chain: E
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*GP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') Chain: F
Molecule details ›
Chain: F
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 44.205Å b: 60.834Å c: 73.619Å
α: 82.55° β: 77.17° γ: 85.85°
R-values:
R R work R free
0.255 0.253 0.274
Expression systems:
  • Escherichia coli
  • Not provided

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