› 5v3h

X-ray diffraction
2.69Å resolution

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: 444 amino acids
Theoretical weight: 51.03 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9NRG4 (Residues: 1-433; Coverage: 100%)
Gene names: KMT3C, SMYD2
Sequence domains:

Ligands and Environments

6 bound ligands:
Ligand SAM 1 x SAM
Ligand ZN 3 x ZN
Ligand 8WG 2 x 8WG
Ligand PEG 2 x PEG
Ligand EDO 1 x EDO
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17B1
Spacegroup: C2
Unit cell:
a: 157.56Å b: 54.775Å c: 79.702Å
α: 90° β: 114.22° γ: 90°
R-values:
R R work R free
0.22 0.218 0.27
Expression system: Spodoptera frugiperda

Quick links

Citations

12 review citations

Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease.
Bhat et al. (2021)
11 more

1 mention without citation

Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation.
Thomenius et al. (2018)