› 6p93

X-ray diffraction
2.1Å resolution

Human APE1 K98A AP-endonuclease product complex

Released:
DOI: 10.2210/pdb6p93/pdb
PDB entry 6p93 coloured by chain, front view.
PDB entry 6p93 coloured by chain, side view.
PDB entry 6p93 coloured by chain, top view.
Source organisms:
Primary publication:
Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance.
McNeill DR, Whitaker AM, Stark WJ, Illuzzi JL, McKinnon PJ, Freudenthal BD, Wilson DM
Mutagenesis 35 27-38 (2020)
PMID: 31816044

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:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120442 (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: 31.13 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: P
Molecule details ›
Chain: P
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: V
Molecule details ›
Chain: V
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand PEG 1 x PEG
Ligand CL 1 x CL
Ligand EDO 4 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 44.351Å b: 60.493Å c: 72.62Å
α: 83.72° β: 79.66° γ: 88.46°
R-values:
R R work R free
0.174 0.172 0.226
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

The multifunctional APE1 DNA repair-redox signaling protein as a drug target in human disease.
Caston et al. (2021)
4 more

1 mention without citation

Functions of the major abasic endonuclease (APE1) in cell viability and genotoxin resistance.
McNeill et al. (2020)