› 3qww

X-ray diffraction
1.8Å resolution

Crystal structure of histone lysine methyltransferase SmyD2 in complex with the methyltransferase inhibitor sinefungin

Released:
DOI: 10.2210/pdb3qww/pdb
PDB entry 3qww coloured by chain, front view.
PDB entry 3qww coloured by chain, side view.
PDB entry 3qww coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Crystal structures of histone and p53 methyltransferase SmyD2 reveal a conformational flexibility of the autoinhibitory C-terminal domain.
Jiang Y, Sirinupong N, Brunzelle J, Yang Z
PLoS One 6 e21640 (2011)
PMID: 21738746

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-185907 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-lysine methyltransferase SMYD2 Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 49.64 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8R5A0 (Residues: 1-433; Coverage: 100%)
Gene name: Smyd2
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 57.52Å b: 75.15Å c: 112.52Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.186 0.208
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Targeting histone lysine methylation in cancer.
McGrath et al. (2015)
6 more

5 mentions without citation

Structure and function of SET and MYND domain-containing proteins.
Spellmon et al. (2015)
4 more