› 5hi7

X-ray diffraction
2.15Å resolution

Co-crystal structure of human SMYD3 with an aza-SAH compound

Released:
DOI: 10.2210/pdb5hi7/pdb
PDB entry 5hi7 coloured by chain, front view.
PDB entry 5hi7 coloured by chain, side view.
PDB entry 5hi7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Based Design of a Novel SMYD3 Inhibitor that Bridges the SAM-and MEKK2-Binding Pockets.
Van Aller GS, Graves AP, Elkins PA, Bonnette WG, McDevitt PJ, Zappacosta F, Annan RS, Dean TW, Su DS, Carpenter CL, Mohammad HP, Kruger RG
Structure 24 774-781 (2016)
PMID: 27066749

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 Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 49.54 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: Q9H7B4 (Residues: 1-428; Coverage: 100%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 3 x ZN
Ligand MG 2 x MG
Ligand DMS 1 x DMS
Ligand 62X 1 x 62X
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 60.47Å b: 66.401Å c: 104.851Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.226
Expression system: unidentified baculovirus

Quick links

Citations

14 review citations

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

2 mentions without citation

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
1 more