› 5kch

X-ray diffraction
1.7Å resolution

SETDB1 in complex with an early stage, low affinity fragment candidate modelled at reduced occupancy into weak electron density

Released:
DOI: 10.2210/pdb5kch/pdb
PDB entry 5kch coloured by chain, front view.
PDB entry 5kch coloured by chain, side view.
PDB entry 5kch coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tempel W, Harding RJ, Mader P, Dobrovetsky E, Walker JR, Brown PJ, Schapira M, Collins P, Pearce N, Brandao-Neto J, Douangamath A, von Delft F, Bountra C, 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: 225 amino acids
Theoretical weight: 26.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q15047 (Residues: 196-403; Coverage: 16%)
Gene names: ESET, KIAA0067, KMT1E, SETDB1
Sequence domains:
Structure domains: SH3 type barrels.

Ligands and Environments

4 bound ligands:
Ligand UNX 50 x UNX
Ligand DMS 1 x DMS
Ligand SO4 2 x SO4
Ligand 6RN 1 x 6RN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 55.967Å b: 63.607Å c: 70.457Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.217 0.215 0.258
Expression system: Escherichia coli BL21(DE3)

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