6mon

X-ray diffraction
2.71Å resolution

Crystal structure of human SMYD2 in complex with Nle-peptide inhibitor

Released:

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)

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-167074 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-lysine methyltransferase SMYD2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 429 amino acids
Theoretical weight: 49.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NRG4 (Residues: 5-433; Coverage: 99%)
Gene names: KMT3C, SMYD2
Sequence domains:
LYS-LEU-NLE-SER-LYS-ARG-GLY Chains: C, D
Molecule details ›
Chains: C, D
Length: 7 amino acids
Theoretical weight: 804 Da
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P42
Unit cell:
a: 153.728Å b: 153.728Å c: 53.457Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.211 0.21 0.227
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided