› 3mek

X-ray diffraction
2.1Å resolution

Crystal Structure of Human Histone-Lysine N-methyltransferase SMYD3 in Complex with S-adenosyl-L-methionine

Released:
DOI: 10.2210/pdb3mek/pdb
PDB entry 3mek coloured by chain, front view.
PDB entry 3mek coloured by chain, side view.
PDB entry 3mek coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Lam R, Dombrovski L, Li Y, Bountra C, Weigelt J, Arrowsmith CH, Edwards AM, Bochkarev A, Min J, Wu H, Structural Genomics Consortium (SGC)

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: 429 amino acids
Theoretical weight: 49.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9H7B4 (Residues: 1-428; Coverage: 100%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand ZN 3 x ZN
Ligand SAM 1 x SAM
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 60.809Å b: 65.923Å c: 108.102Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.174 0.208
Expression system: Escherichia coli

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