PDBe 4qbr

X-ray diffraction
1.9Å resolution

Crystal structure of DNMT3a ADD domain G550D mutant bound to H3 peptide

Released:
Source organism: Homo sapiens
Entry authors: Wang H, Li H

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
DNA (cytosine-5)-methyltransferase 3A Chains: A, C
Molecule details ›
Chains: A, C
Length: 137 amino acids
Theoretical weight: 15.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW Q9Y6K1 (Residues: 476-611; Coverage: 15%)
Gene name: DNMT3A
Histone H3.1 Chains: E, P
Molecule details ›
Chains: E, P
Length: 7 amino acids
Theoretical weight: 777 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: NEW P68431 (Residues: 2-8; Coverage: 5%)
Gene names: H3FA, H3FB, H3FC, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P1
Unit cell:
a: 36.057Å b: 37.161Å c: 50.125Å
α: 78.7° β: 83.89° γ: 81.56°
R-values:
R R work R free
0.18 0.178 0.225
Expression systems:
  • Escherichia coli
  • Not provided