› 5ke2

X-ray diffraction
1.56Å resolution

Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A

Released:
DOI: 10.2210/pdb5ke2/pdb
PDB entry 5ke2 coloured by chain, front view.
PDB entry 5ke2 coloured by chain, side view.
PDB entry 5ke2 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dong A, Iqbal A, Mader P, Dobrovetsky E, Walker JR, Bountra C, Arrowsmith CH, Edwards AM, Brown PJ, Structural Genomics Consortium (SGC)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-N(6),N(6)-dimethyl-L-lysine(9) = S-adenosyl-L-homocysteine + a [histone H3]-N(6),N(6),N(6)-trimethyl-L-lysine(9)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-172172 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase SETDB1 Chain: A
Molecule details ›
Chain: A
Length: 213 amino acids
Theoretical weight: 24.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15047 (Residues: 196-402; Coverage: 16%)
Gene names: ESET, KIAA0067, KMT1E, SETDB1
Sequence domains:
Structure domains: SH3 type barrels.

Ligands and Environments

4 bound ligands:
Ligand 6S4 1 x 6S4
Ligand EDO 2 x EDO
Ligand SO4 6 x SO4
Ligand UNX 8 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 54.816Å b: 63.891Å c: 69.793Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.191 0.218
Expression system: Escherichia coli BL21(DE3)

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