PDBe 5ex3

X-ray diffraction
2.41Å resolution

Crystal structure of human SMYD3 in complex with a VEGFR1 peptide


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]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
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 Chain: A
Molecule details ›
Chain: A
Length: 436 amino acids
Theoretical weight: 49.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt: Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:
Vascular endothelial growth factor receptor 1 Chain: D
Molecule details ›
Chain: D
Length: 9 amino acids
Theoretical weight: 1 KDa
Source organism: Homo sapiens
Expression system: Not provided
  • Canonical: NEW P17948 (Residues: 827-835; Coverage: 1%)
Gene names: FLT, FLT1, FRT, VEGFR1

Ligands and Environments

Cofactor: Ligand SAH 1 x SAH
2 bound ligands:

1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U
Spacegroup: P212121
Unit cell:
a: 53.378Å b: 104.659Å c: 117.599Å
α: 90° β: 90° γ: 90°
R R work R free
0.187 0.184 0.223
Expression systems:
  • Escherichia coli
  • Not provided