› 3rib

X-ray diffraction
2.79Å resolution

Human lysine methyltransferase Smyd2 in complex with AdoHcy

Released:
DOI: 10.2210/pdb3rib/pdb
PDB entry 3rib coloured by chain, front view.
PDB entry 3rib coloured by chain, side view.
PDB entry 3rib coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins.
Xu S, Zhong C, Zhang T, Ding J
J Mol Cell Biol 3 293-300 (2011)
PMID: 21724641

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 Chains: A, B
Molecule details ›
Chains: A, B
Length: 441 amino acids
Theoretical weight: 50.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NRG4 (Residues: 1-433; Coverage: 100%)
Gene names: KMT3C, SMYD2
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand SAH 2 x SAH
Ligand SO4 9 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: C2
Unit cell:
a: 194.56Å b: 57.185Å c: 96.607Å
α: 90° β: 103.95° γ: 90°
R-values:
R R work R free
0.248 0.246 0.3
Expression system: Escherichia coli

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

2 mentions without citation

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