PDBe 5hq8

X-ray diffraction
1.72Å resolution

Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A


Function and Biology Details

Reactions catalysed:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase SMYD3 Chains: A, B
Molecule details ›
Chains: A, B
Length: 432 amino acids
Theoretical weight: 49.54 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt: Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:
Mitogen-activated protein kinase kinase kinase 2 Chains: I, J
Molecule details ›
Chains: I, J
Length: 16 amino acids
Theoretical weight: 1.74 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: NEW Q9Y2U5 (Residues: 250-264; Coverage: 2%)
Gene names: MAP3K2, MAPKKK2, MEKK2

Ligands and Environments

Cofactor: Ligand SAH 2 x SAH

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 53.109Å b: 118.155Å c: 84.782Å
α: 90° β: 90.61° γ: 90°
R R work R free
0.176 0.174 0.201
Expression systems:
  • unidentified baculovirus
  • Not provided