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HUMAN APE1 ENDONUCLEASE WITH BOUND ABASIC DNA AND MN2+ ION

X-ray diffraction
3Å resolution
PDB entry 1de9 coloured by chain, front view.
PDB entry 1de9 coloured by chain, side view.
PDB entry 1de9 coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
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: 13426.01 Å2
Buried surface area: 3658.79 Å2
Dissociation area: 1,110.79 Å2
Dissociation energy (ΔGdiss): 10.08 kcal/mol
Dissociation entropy (TΔSdiss): 16.54 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-113675
Assembly 2
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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: 13361.12 Å2
Buried surface area: 3667.73 Å2
Dissociation area: 1,106.57 Å2
Dissociation energy (ΔGdiss): -0.89 kcal/mol
Dissociation entropy (TΔSdiss): 16.57 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-113675

Macromolecules

DNA repair nuclease/redox regulator APEX1, mitochondrial
Chains: A, B
Length: 276 amino acids
Theoretical weight: 31.2 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
Pfam: Endonuclease/Exonuclease/phosphatase family
InterPro:
CATH: Endonuclease/exonuclease/phosphatase
SCOP: DNase I-like
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 1de9, assembly 1, front view.
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 1de9, assembly 1, side view.
DNA repair nuclease/redox regulator APEX1, mitochondrial in PDB entry 1de9, assembly 1, top view.
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DNA chains U, X
Name: 5'-d(*CP*TP*AP*C)-3'
Representative chains: U, X
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 4 nucleotides
Theoretical weight: 1.15 KDa
5'-d(*CP*TP*AP*C)-3' in PDB entry 1de9, assembly 1, front view.
5'-d(*CP*TP*AP*C)-3' in PDB entry 1de9, assembly 1, side view.
5'-d(*CP*TP*AP*C)-3' in PDB entry 1de9, assembly 1, top view.
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DNA chains V, Y
Name: 5'-d(P*(3DR)P*GP*AP*TP*C)-3'
Representative chains: V, Y
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 5 nucleotides
Theoretical weight: 1.37 KDa
5'-d(P*(3DR)P*GP*AP*TP*C)-3' in PDB entry 1de9, assembly 1, front view.
5'-d(P*(3DR)P*GP*AP*TP*C)-3' in PDB entry 1de9, assembly 1, side view.
5'-d(P*(3DR)P*GP*AP*TP*C)-3' in PDB entry 1de9, assembly 1, top view.
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DNA chains W, Z
Name: 5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3'
Representative chains: W, Z
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' in PDB entry 1de9, assembly 1, front view.
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' in PDB entry 1de9, assembly 1, side view.
5'-d(*GP*AP*TP*CP*GP*GP*TP*AP*G)-3' in PDB entry 1de9, assembly 1, top view.
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