› 3t3y

X-ray diffraction
2Å resolution

Crystal structure of AlkB in complex with Fe(III) and 2-(3-hydroxypicolinomido)acetic acid

Released:
DOI: 10.2210/pdb3t3y/pdb
PDB entry 3t3y coloured by chain, front view.
PDB entry 3t3y coloured by chain, side view.
PDB entry 3t3y coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Dynamic combinatorial mass spectrometry leads to inhibitors of a 2-oxoglutarate-dependent nucleic acid demethylase.
Woon EC, Demetriades M, Bagg EA, Aik W, Krylova SM, Ma JH, Chan M, Walport LJ, Wegman DW, Dack KN, McDonough MA, Krylov SN, Schofield CJ
J Med Chem 55 2173-84 (2012)
PMID: 22263962

Function and Biology Details

Reaction catalysed: 
DNA-base-CH(3) + 2-oxoglutarate + O(2) = DNA-base + formaldehyde + succinate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-138340 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Alpha-ketoglutarate-dependent dioxygenase AlkB Chain: A
Molecule details ›
Chain: A
Length: 206 amino acids
Theoretical weight: 22.95 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P05050 (Residues: 12-216; Coverage: 95%)
Gene names: JW2200, aidD, alkB, b2212
Structure domains: Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Ligands and Environments

2 bound ligands:
Ligand FE 1 x FE
Ligand MD6 1 x MD6
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P1
Unit cell:
a: 36.813Å b: 38.594Å c: 40.487Å
α: 71.25° β: 72.21° γ: 66.7°
R-values:
R R work R free
0.184 0.182 0.221
Expression system: Escherichia coli

Quick links

Citations

12 review citations

N6-methyladenosine links RNA metabolism to cancer progression.
Dai et al. (2018)
11 more