› 5teg

X-ray diffraction
1.3Å resolution

Crystal structure of hSETD8 in complex with histone H4K20 norleucine mutant peptide and S-Adenosylmethionine

Released:
DOI: 10.2210/pdb5teg/pdb
PDB entry 5teg coloured by chain, front view.
PDB entry 5teg coloured by chain, side view.
PDB entry 5teg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Turning a Substrate Peptide into a Potent Inhibitor for the Histone Methyltransferase SETD8.
Judge RA, Zhu H, Upadhyay AK, Bodelle PM, Hutchins CW, Torrent M, Marin VL, Yu W, Vedadi M, Li F, Brown PJ, Pappano WN, Sun C, Petros AM
ACS Med Chem Lett 7 1102-1106 (2016)
PMID: 27994746

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158688 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-lysine methyltransferase KMT5A Chains: A, B
Molecule details ›
Chains: A, B
Length: 160 amino acids
Theoretical weight: 18.21 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NQR1 (Residues: 234-393; Coverage: 41%)
Gene names: KMT5A, PRSET7, SET07, SET8, SETD8
Sequence domains: SET domain
Structure domains: SET domain
Histone H4 Chains: D, E
Molecule details ›
Chains: D, E
Length: 8 amino acids
Theoretical weight: 1.08 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 17-24; Coverage: 8%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4

Ligands and Environments

1 bound ligand:
Ligand SAM 2 x SAM
1 modified residue:
Ligand NLE 2 x NLE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P1
Unit cell:
a: 44.31Å b: 45.059Å c: 52.649Å
α: 114.73° β: 90.77° γ: 90.81°
R-values:
R R work R free
0.191 0.189 0.21
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

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

3 mentions without citation

Turning a Substrate Peptide into a Potent Inhibitor for the Histone Methyltransferase SETD8.
Judge et al. (2016)
2 more