› 5w1y

X-ray diffraction
1.7Å resolution

SETD8 in complex with a covalent inhibitor

Released:
DOI: 10.2210/pdb5w1y/pdb
PDB entry 5w1y coloured by chain, front view.
PDB entry 5w1y coloured by chain, side view.
PDB entry 5w1y coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Tempel W, Yu W, Li Y, Blum G, Luo M, Pittella-Silva F, Bountra C, Arrowsmith CH, Edwards AM, Brown PJ, Structural Genomics Consortium (SGC)

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H4]-L-lysine(20) = S-adenosyl-L-homocysteine + a [histone H4]-N(6)-methyl-L-lysine(20)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-192510 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-lysine methyltransferase KMT5A Chains: A, B
Molecule details ›
Chains: A, B
Length: 166 amino acids
Theoretical weight: 18.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9NQR1 (Residues: 232-393; Coverage: 41%)
Gene names: KMT5A, PRSET7, SET07, SET8, SETD8
Sequence domains: SET domain
Structure domains: SET domain

Ligands and Environments

2 bound ligands:
Ligand 9SV 2 x 9SV
Ligand UNX 36 x UNX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 58.348Å b: 39.788Å c: 131.895Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.202 0.201 0.237
Expression system: Escherichia coli BL21

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