› 4qhe

X-ray diffraction
1.4Å resolution

Crystal structure of Mg2+ bound human APE1

Released:
DOI: 10.2210/pdb4qhe/pdb
PDB entry 4qhe coloured by chain, front view.
PDB entry 4qhe coloured by chain, side view.
PDB entry 4qhe coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I.
He H, Chen Q, Georgiadis MM
Biochemistry 53 6520-9 (2014)
PMID: 25251148

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
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151054 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA repair nuclease/redox regulator APEX1, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 285 amino acids
Theoretical weight: 32.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 38-318; Coverage: 88%)
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:
Ligand MG 1 x MG
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 46.491Å b: 137.545Å c: 45.054Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.193
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Inhibition of APE1/Ref-1 for Neovascular Eye Diseases: From Biology to Therapy.
Hartman et al. (2021)
1 more

10 mentions without citation

Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain.
López et al. (2021)
9 more