› 3s5a

X-ray diffraction
1.7Å resolution

ABH2 cross-linked to undamaged dsDNA-2 with cofactors

Released:
DOI: 10.2210/pdb3s5a/pdb
PDB entry 3s5a coloured by chain, front view.
PDB entry 3s5a coloured by chain, side view.
PDB entry 3s5a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Duplex interrogation by a direct DNA repair protein in search of base damage.
Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C
Nat Struct Mol Biol 19 671-6 (2012)
PMID: 22659876

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-116864 (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: 204 amino acids
Theoretical weight: 23.27 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
5'-D(*CP*TP*GP*TP*CP*TP*CP*AP*CP*TP*GP*TP*CP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 14 nucleotides
Theoretical weight: 4.22 KDa
Source organism: Homo sapiens
Expression system: Not provided
5'-D(*TP*CP*GP*AP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 14 nucleotides
Theoretical weight: 4.31 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MN 1 x MN
Ligand AKG 1 x AKG
Ligand GOL 3 x GOL
Ligand XL3 1 x XL3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 45.968Å b: 60.61Å c: 65.588Å
α: 90° β: 90.52° γ: 90°
R-values:
R R work R free
0.199 0.197 0.238
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

16 review citations

Bacterial sigma factors: a historical, structural, and genomic perspective.
Feklístov et al. (2014)
15 more

4 mentions without citation

Duplex interrogation by a direct DNA repair protein in search of base damage.
Yi et al. (2012)
3 more