› 3qkj

X-ray diffraction
2.04Å resolution

The PWWP domain of human DNA (CYTOSINE-5-)-METHYLTRANSFERASE 3 BETA in complex with a bis-tris molecule

Released:
DOI: 10.2210/pdb3qkj/pdb
PDB entry 3qkj coloured by chain, front view.
PDB entry 3qkj coloured by chain, side view.
PDB entry 3qkj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and histone binding ability characterizations of human PWWP domains.
Wu H, Zeng H, Lam R, Tempel W, Amaya MF, Xu C, Dombrovski L, Qiu W, Wang Y, Min J
PLoS One 6 e18919 (2011)
PMID: 21720545

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193641 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA (cytosine-5)-methyltransferase 3B Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 151 amino acids
Theoretical weight: 16.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9UBC3 (Residues: 206-355; Coverage: 18%)
Gene name: DNMT3B
Sequence domains: PWWP domain
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand BTB 4 x BTB
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P32
Unit cell:
a: 74.544Å b: 74.544Å c: 160.266Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.21 0.209 0.228
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

27 review citations

Perceiving the epigenetic landscape through histone readers.
Musselman et al. (2012)
26 more

5 mentions without citation

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