Crystal structure of YTHDF2 in complex with M6AM

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 30% strand (DSSP).

Ligands and binding sites

• TV8 · (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-4-methoxy-5-[6-(methylamino)purin-9-yl]oxolan-3-ol · ligand · chains A, B
• SO4 · Sulfate ion · ion · 7 copies · chains A, B
• GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 461 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7BIK · Crystal structure of YTHDF2 in complex with m6Am · the same entry in another collection · chain A against A, TM-score 1.00
• Q9Y5A9 · AlphaFold monomer V2.0 prediction for yth domain-containing family protein 2 (Q9Y5A9) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 Q9Y5A9
• Elsewhere: RCSB PDB 7BIK · PDBe 7BIK · UniProt Q9Y5A9