› 5xxd

X-ray diffraction
2.31Å resolution

Crystal structure of SmyD3 in complex with covalent inhibitor 1

Released:
DOI: 10.2210/pdb5xxd/pdb
PDB entry 5xxd coloured by chain, front view.
PDB entry 5xxd coloured by chain, side view.
PDB entry 5xxd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Baburajendran N, Anna E J

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: 423 amino acids
Theoretical weight: 48.6 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H7B4 (Residues: 3-425; Coverage: 99%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand SAM 1 x SAM
Ligand ZN 3 x ZN
Ligand 8NR 1 x 8NR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007
Spacegroup: P212121
Unit cell:
a: 61.458Å b: 66.472Å c: 107.062Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.201 0.259
Expression system: Escherichia coli

Quick links