› 3oxf

X-ray diffraction
2.82Å resolution

Human lysine methyltransferase Smyd3 in complex with AdoHcy (Form I)

Released:
DOI: 10.2210/pdb3oxf/pdb
PDB entry 3oxf coloured by chain, front view.
PDB entry 3oxf coloured by chain, side view.
PDB entry 3oxf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.
Xu S, Wu J, Sun B, Zhong C, Ding J
OpenAccess logo Nucleic Acids Res 39 4438-49 (2011)
PMID: 21266482

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: 436 amino acids
Theoretical weight: 50.25 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H7B4 (Residues: 1-428; Coverage: 100%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P21
Unit cell:
a: 57.991Å b: 117.99Å c: 82.808Å
α: 90° β: 91.78° γ: 90°
R-values:
R R work R free
0.213 0.211 0.261
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Targeting histone lysine methylation in cancer.
McGrath et al. (2015)
13 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