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Human APE1 product complex

X-ray diffraction
1.57Å resolution
PDB entry 5dff coloured by chain, front view.
PDB entry 5dff coloured by chain, side view.
PDB entry 5dff coloured by chain, top view.
Source organisms:
Assemblies composition:
hetero tetramer (preferred)
monomeric
Entry contents: 1 distinct polypeptide molecule
3 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA repair nuclease/redox regulator APEX1 and DNA
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Multimeric state: hetero tetramer
Accessible surface area: 17746.98 Å2
Buried surface area: 5923.45 Å2
Dissociation area: 1,485.56 Å2
Dissociation energy (ΔGdiss): 9.86 kcal/mol
Dissociation entropy (TΔSdiss): 12.31 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-118562
Assembly 2
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Assembly Name: DNA repair nuclease/redox regulator APEX1
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Multimeric state: monomeric
Accessible surface area: 12066.94 Å2
Buried surface area: 645.35 Å2
Dissociation area: 120.78 Å2
Dissociation energy (ΔGdiss): -4.45 kcal/mol
Dissociation entropy (TΔSdiss): -0.33 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-151054

Macromolecules

DNA repair nuclease/redox regulator APEX1, mitochondrial
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.19 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27695 (Residues: 43-318; Coverage: 87%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Pfam: Endonuclease/Exonuclease/phosphatase family
InterPro:
CATH: Endonuclease/exonuclease/phosphatase
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 5dff, assembly 1, front view.
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 5dff, assembly 1, side view.
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 5dff, assembly 1, top view.
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DNA chain D
Name: DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3')
Representative chains: D
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 11 nucleotides
Theoretical weight: 3.21 KDa
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') in PDB entry 5dff, assembly 1, front view.
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') in PDB entry 5dff, assembly 1, side view.
DNA (5'-D(P*(3DR)P*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') in PDB entry 5dff, assembly 1, top view.
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DNA chain P
Name: DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')
Representative chains: P
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 10 nucleotides
Theoretical weight: 3.06 KDa
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 5dff, assembly 1, front view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 5dff, assembly 1, side view.
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') in PDB entry 5dff, assembly 1, top view.
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DNA chain V
Name: 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')
Representative chains: V
Source organism: synthetic construct [32630]
Expression system: Not provided
Length: 21 nucleotides
Theoretical weight: 6.47 KDa
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') in PDB entry 5dff, assembly 1, front view.
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') in PDB entry 5dff, assembly 1, side view.
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') in PDB entry 5dff, assembly 1, top view.
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