› 5kh6

X-ray diffraction
2.05Å resolution

SETDB1 in complex with a fragment candidate

Released:
DOI: 10.2210/pdb5kh6/pdb
PDB entry 5kh6 coloured by chain, front view.
PDB entry 5kh6 coloured by chain, side view.
PDB entry 5kh6 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Walker JR, Harding RJ, Mader P, Dobrovetsky E, Dong A, Collins P, Pearce N, Brandao-Neto J, Douangamath A, von Delft F, Brown PJ, Schapira M, Arrowsmith CH, Edwards AM, Santhakumar V, 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: 211 amino acids
Theoretical weight: 24.63 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15047 (Residues: 196-400; Coverage: 16%)
Gene names: ESET, KIAA0067, KMT1E, SETDB1
Sequence domains:
Structure domains: SH3 type barrels.

Ligands and Environments

8 bound ligands:
Ligand EDO 4 x EDO
Ligand DMS 1 x DMS
Ligand SO4 5 x SO4
Ligand CL 4 x CL
Ligand 6SU 1 x 6SU
Ligand PEG 3 x PEG
Ligand ACT 1 x ACT
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 55.76Å b: 63.81Å c: 70.31Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.235
Expression system: Escherichia coli BL21(DE3)

Quick links