› 5eg2

X-ray diffraction
1.55Å resolution

SET7/9 N265A in complex with AdoHcy and TAF10 peptide

Released:
DOI: 10.2210/pdb5eg2/pdb
PDB entry 5eg2 coloured by chain, front view.
PDB entry 5eg2 coloured by chain, side view.
PDB entry 5eg2 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Sulfur-Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9.
Fick RJ, Kroner GM, Nepal B, Magnani R, Horowitz S, Houtz RL, Scheiner S, Trievel RC
ACS Chem Biol 11 748-54 (2016)
PMID: 26713889

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171459 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Histone-lysine N-methyltransferase SETD7 Chain: A
Molecule details ›
Chain: A
Length: 262 amino acids
Theoretical weight: 29.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8WTS6 (Residues: 110-366; Coverage: 70%)
Gene names: KIAA1717, KMT7, SET7, SET9, SETD7
Sequence domains:
Structure domains:
Transcription initiation factor TFIID subunit 10 Chain: B
Molecule details ›
Chain: B
Length: 10 amino acids
Theoretical weight: 1.24 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q12962 (Residues: 186-195; Coverage: 5%)
Gene names: TAF10, TAF2A, TAF2H, TAFII30

Ligands and Environments

2 bound ligands:
Ligand SAH 1 x SAH
Ligand NA 1 x NA
1 modified residue:
Ligand MLZ 1 x MLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P3221
Unit cell:
a: 83.198Å b: 83.198Å c: 95.859Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.148 0.147 0.171
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Chalcogen Bonding: An Overview.
Vogel et al. (2019)
5 more

1 mention without citation

Deep Neural Network Classifier for Virtual Screening Inhibitors of (S)-Adenosyl-L-Methionine (SAM)-Dependent Methyltransferase Family.
Li et al. (2019)