› 4qbq

X-ray diffraction
2.41Å resolution

Crystal structure of DNMT3a ADD domain bound to H3 peptide

Released:
DOI: 10.2210/pdb4qbq/pdb
PDB entry 4qbq coloured by chain, front view.
PDB entry 4qbq coloured by chain, side view.
PDB entry 4qbq coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Li H, Patel DJ

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:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159455 (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: 15.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y6K1 (Residues: 479-610; Coverage: 15%)
Gene name: DNMT3A
Sequence domains:
Histone H3.1 Chain: P
Molecule details ›
Chain: P
Length: 8 amino acids
Theoretical weight: 934 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P68431 (Residues: 2-9; Coverage: 6%)
Gene names: H3C1, H3C10, H3C11, H3C12, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3FA, H3FB, H3FC HIST1H3C, H3FD, H3FF, H3FH, H3FI, H3FJ, H3FK, H3FL, HIST1H3A, HIST1H3B, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 41.557Å b: 56.424Å c: 57.301Å
α: 90° β: 90.27° γ: 90°
R-values:
R R work R free
0.176 0.174 0.23
Expression systems:
  • Escherichia coli
  • Not provided

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