› 5wcg

X-ray diffraction
2.02Å resolution

SET and MYND Domain Containing protein 2

Released:
DOI: 10.2210/pdb5wcg/pdb
PDB entry 5wcg coloured by chain, front view.
PDB entry 5wcg coloured by chain, side view.
PDB entry 5wcg coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Zeng H, Walker JR, Hutch A, Seitova A, Tatlock J, Kumpf R, Owen A, Taylor A, Casimiro-Garcia A, Bountra C, Arrowsmith CH, Edwards AM, Brown PJ, 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-192559 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-lysine methyltransferase SMYD2 Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 49.83 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: Q9NRG4 (Residues: 1-433; Coverage: 100%)
Gene names: KMT3C, SMYD2
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand A4M 1 x A4M
Ligand DMS 1 x DMS
Ligand TRS 1 x TRS
Ligand UNX 5 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: C2
Unit cell:
a: 92.343Å b: 98.312Å c: 58.833Å
α: 90° β: 101.95° γ: 90°
R-values:
R R work R free
0.171 0.17 0.213
Expression system: unidentified baculovirus

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