› 3a1a

X-ray diffraction
2.3Å resolution

Crystal Structure of the DNMT3A ADD domain

Released:
DOI: 10.2210/pdb3a1a/pdb
PDB entry 3a1a coloured by chain, front view.
PDB entry 3a1a coloured by chain, side view.
PDB entry 3a1a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain.
Otani J, Nankumo T, Arita K, Inamoto S, Ariyoshi M, Shirakawa M
EMBO Rep 10 1235-41 (2009)
PMID: 19834512

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-195368 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 3A Chain: A
Molecule details ›
Chain: A
Length: 144 amino acids
Theoretical weight: 16.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y6K1 (Residues: 476-614; Coverage: 15%)
Gene name: DNMT3A
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P6122
Unit cell:
a: 57.581Å b: 57.581Å c: 138.949Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.211 0.209 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

96 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
95 more

8 mentions without citation

Modulation of epigenetic targets for anticancer therapy: clinicopathological relevance, structural data and drug discovery perspectives.
Andreoli et al. (2013)
7 more