› 4mgt

X-ray diffraction
2.6Å resolution

ALKBH2 R110A cross-linked to undamaged dsDNA

Released:
DOI: 10.2210/pdb4mgt/pdb
PDB entry 4mgt coloured by chain, front view.
PDB entry 4mgt coloured by chain, side view.
PDB entry 4mgt coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin
Chen B, Gan J, Yang CG
Sci China Chem 57 307-313 (2014)

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
  • not assigned
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117849 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA oxidative demethylase ALKBH2 Chain: A
Molecule details ›
Chain: A
Length: 205 amino acids
Theoretical weight: 23.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6NS38 (Residues: 56-258; Coverage: 78%)
Gene names: ABH2, ALKBH2
Sequence domains: 2OG-Fe(II) oxygenase superfamily
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like
DNA1 Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Homo sapiens
Expression system: Not provided
DNA2 Chain: C
Molecule details ›
Chain: C
Length: 13 nucleotides
Theoretical weight: 3.99 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P6322
Unit cell:
a: 129.099Å b: 129.099Å c: 84.466Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.233 0.231 0.276
Expression systems:
  • Escherichia coli
  • Not provided

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