Crystal structure of human PRMT6 in complex with S-adenosyl-L- homocysteine and YS17-117 compound

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 35% strand (DSSP).

Ligands and binding sites

• SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
• O3P · N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]prop-2-enamide · ligand · 3 copies · chains A, B, C
• O3S · N-[3-(4-{[(2-aminoethyl)(methyl)amino]methyl}-1H-pyrrol-3-yl)phenyl]propanamide · ligand · chains D
• GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Interfaces

6 interfaces between chains.

• B–C · 1845 Ų buried · 19 hydrogen bonds · protein-protein
• A–D · 1794 Ų buried · 17 hydrogen bonds · protein-protein
• A–B · 556 Ų buried · 7 hydrogen bonds · protein-protein
• C–D · 550 Ų buried · 8 hydrogen bonds · protein-protein
• B–D · 136 Ų buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 6P7I · Crystal structure of Human PRMT6 in complex with S-Adenosyl-L-Homocysteine and YS17-117… · the same entry in another collection · chain D against D, TM-score 1.00
• Q96LA8 · AlphaFold monomer V2.0 prediction for protein arginine N-methyltransferase 6 (Q96LA8) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 Q96LA8
• Elsewhere: RCSB PDB 6P7I · PDBe 6P7I · UniProt Q96LA8