› 6bor

X-ray diffraction
1.84Å resolution

Human APE1 substrate complex with an G/G mismatch adjacent the THF

Released:
DOI: 10.2210/pdb6bor/pdb
PDB entry 6bor coloured by chain, front view.
PDB entry 6bor coloured by chain, side view.
PDB entry 6bor coloured by chain, top view.
Source organisms:
Primary publication:
Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Fairlamb MS, Whitaker AM, Freudenthal BD
Acta Crystallogr D Struct Biol 74 760-768 (2018)
PMID: 30082511

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:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-119615 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA repair nuclease/redox regulator APEX1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 318 amino acids
Theoretical weight: 35.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P27695 (Residues: 1-318; Coverage: 100%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Sequence domains: Endonuclease/Exonuclease/phosphatase family
Structure domains: Endonuclease/exonuclease/phosphatase
21-mer DNA Chain: P
Molecule details ›
Chain: P
Length: 21 nucleotides
Theoretical weight: 6.36 KDa
Source organism: synthetic construct
Expression system: Not provided
21-mer DNA Chain: V
Molecule details ›
Chain: V
Length: 21 nucleotides
Theoretical weight: 6.45 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P1
Unit cell:
a: 44.408Å b: 60.204Å c: 73.014Å
α: 82.94° β: 80.29° γ: 89.1°
R-values:
R R work R free
0.172 0.17 0.209
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

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

1 mention without citation

Apurinic/apyrimidinic (AP) endonuclease 1 processing of AP sites with 5' mismatches.
Fairlamb et al. (2018)