› 3ru0

X-ray diffraction
1.85Å resolution

Cocrystal structure of human SMYD3 with inhibitor Sinefungin bound

Released:
DOI: 10.2210/pdb3ru0/pdb
PDB entry 3ru0 coloured by chain, front view.
PDB entry 3ru0 coloured by chain, side view.
PDB entry 3ru0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and functional profiling of the human histone methyltransferase SMYD3.
Foreman KW, Brown M, Park F, Emtage S, Harriss J, Das C, Zhu L, Crew A, Arnold L, Shaaban S, Tucker P
PLoS One 6 e22290 (2011)
PMID: 21779408

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-190659 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase SMYD3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 438 amino acids
Theoretical weight: 50.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9H7B4 (Residues: 2-428; Coverage: 100%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand SFG 2 x SFG
Ligand ZN 6 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P21
Unit cell:
a: 58.175Å b: 118.073Å c: 82.901Å
α: 90° β: 91.58° γ: 90°
R-values:
R R work R free
0.2 0.2 0.216
Expression system: Spodoptera frugiperda

Quick links

Citations

24 review citations

Critical roles of non-histone protein lysine methylation in human tumorigenesis.
Hamamoto et al. (2015)
23 more

3 mentions without citation

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