Crystal structure of SETDB1 tudor domain with aryl triazole fragment peptide conjugates

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 47% strand (DSSP).

Ligands and binding sites

• E2G · (2R)-N-[(4-{2-[(acetylamino)methyl]phenyl}-5-methyl-4H-1,2,4-triazol-3-yl)methyl]-2-amino-2-hydroxyacetamide · ligand · chains A, B
• SO4 · Sulfate ion · ion · 4 copies · chains A, B
• UNX · Unknown atom or ion · ion · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 324 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, methylation).

Compared structures

• 6BPI · Crystal structure of SETDB1 Tudor domain with aryl triazole fragment peptide conjugates · the same entry in another collection · chain A against A, TM-score 1.00
• Q15047 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETDB1 (Q15047) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt Q15047
• Elsewhere: RCSB PDB 6BPI · PDBe 6BPI · UniProt Q15047