› 4fmu

X-ray diffraction
2.1Å resolution

Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF

Released:
DOI: 10.2210/pdb4fmu/pdb
PDB entry 4fmu coloured by chain, front view.
PDB entry 4fmu coloured by chain, side view.
PDB entry 4fmu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sinefungin derivatives as inhibitors and structure probes of protein lysine methyltransferase SETD2.
Zheng W, Ibáñez G, Wu H, Blum G, Zeng H, Dong A, Li F, Hajian T, Allali-Hassani A, Amaya MF, Siarheyeva A, Yu W, Brown PJ, Schapira M, Vedadi M, Min J, Luo M
J Am Chem Soc 134 18004-14 (2012)
PMID: 23043551

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(36) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(36)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189845 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase SETD2 Chain: A
Molecule details ›
Chain: A
Length: 278 amino acids
Theoretical weight: 31.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9BYW2 (Residues: 1434-1711; Coverage: 11%)
Gene names: HIF1, HSPC069, HYPB, KIAA1732, KMT3A, SET2, SETD2
Sequence domains:
Structure domains: SET domain

Ligands and Environments

3 bound ligands:
Ligand ZN 3 x ZN
Ligand 0UM 1 x 0UM
Ligand UNX 13 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 51.547Å b: 77.277Å c: 78.864Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.194 0.235
Expression system: Escherichia coli

Quick links

Citations

20 review citations

SAM/SAH Analogs as Versatile Tools for SAM-Dependent Methyltransferases.
Zhang et al. (2016)
19 more

9 mentions without citation

Inhibitors of Protein Methyltransferases and Demethylases.
Kaniskan et al. (2018)
8 more