› 3tg4

X-ray diffraction
2Å resolution

Structure of SMYD2 in complex with SAM

Released:
DOI: 10.2210/pdb3tg4/pdb
PDB entry 3tg4 coloured by chain, front view.
PDB entry 3tg4 coloured by chain, side view.
PDB entry 3tg4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human SMYD2 protein reveals the basis of p53 tumor suppressor methylation.
Wang L, Li L, Zhang H, Luo X, Dai J, Zhou S, Gu J, Zhu J, Atadja P, Lu C, Li E, Zhao K
J Biol Chem 286 38725-38737 (2011)
PMID: 21880715

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-192559 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-lysine methyltransferase SMYD2 Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 49.76 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NRG4 (Residues: 1-433; Coverage: 100%)
Gene names: KMT3C, SMYD2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SAM 1 x SAM
Ligand ZN 3 x ZN
Ligand GOL 5 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 52.48Å b: 67.48Å c: 141.97Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.19 0.224
Expression system: Spodoptera frugiperda

Quick links

Citations

10 review citations

SET for life: biochemical activities and biological functions of SET domain-containing proteins.
Herz et al. (2013)
9 more

8 mentions without citation

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