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X-ray structure of human ABH2 bound to dsDNA with Mn(II) and 2KG

X-ray diffraction
2.59Å resolution
PDB entry 3buc coloured by chain, front view.
PDB entry 3buc coloured by chain, side view.
PDB entry 3buc coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero trimer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA oxidative demethylase ALKBH2 and DNA
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Multimeric state: hetero trimer
Accessible surface area: 13062.03 Å2
Buried surface area: 4388.3 Å2
Dissociation area: 1,067.45 Å2
Dissociation energy (ΔGdiss): 16.41 kcal/mol
Dissociation entropy (TΔSdiss): 10.41 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-116112

Macromolecules

DNA oxidative demethylase ALKBH2
Chain: A
Length: 203 amino acids
Theoretical weight: 23.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NS38 (Residues: 56-258; Coverage: 78%)
Gene names: ABH2, ALKBH2
Pfam: 2OG-Fe(II) oxygenase superfamily
InterPro:
CATH: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA oxidative demethylase ALKBH2 in PDB entry 3buc, assembly 1, front view.
DNA oxidative demethylase ALKBH2 in PDB entry 3buc, assembly 1, side view.
DNA oxidative demethylase ALKBH2 in PDB entry 3buc, assembly 1, top view.
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DNA chain B
Name: DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3')
Representative chains: B
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3') in PDB entry 3buc, assembly 1, front view.
DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3') in PDB entry 3buc, assembly 1, side view.
DNA (5'-D(*DCP*DTP*DGP*DTP*DAP*DTP*(MA7)P*DAP*DCP*DTP*DGP*DCP*DG)-3') in PDB entry 3buc, assembly 1, top view.
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DNA chain C
Name: DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3')
Representative chains: C
Source organism: Homo sapiens [9606]
Expression system: Not provided
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3') in PDB entry 3buc, assembly 1, front view.
DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3') in PDB entry 3buc, assembly 1, side view.
DNA (5'-D(*DTP*DCP*DGP*DCP*DAP*DGP*DTP*DTP*DAP*DTP*DAP*DCP*DA)-3') in PDB entry 3buc, assembly 1, top view.
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