Murine SMPDL3A in complex with ADP analog ampcp

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).

Ligands and binding sites

• AP2 · Phosphomethylphosphonic acid adenosyl ester · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A
• FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
• MAN · alpha-D-mannopyranose · sugar · 2 copies
• BMA · beta-D-mannopyranose · sugar
• ZN · Zinc ion · metal · 2 copies · chains A
• GOL · Glycerol · additive · 4 copies · chains A

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

Pockets

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

Modifications

Observed in the structure: 4 glycan, 3 disulfide (N-glycosylation, disulfide).

Compared structures

• 5FC6 · Murine SMPDL3A in complex with ADP analog AMPCP · the same entry in another collection · chain A against A, TM-score 1.00
• P70158 · AlphaFold monomer V2.0 prediction for acid sphingomyelinase-like phosphodiesterase 3A… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P70158
• Elsewhere: RCSB PDB 5FC6 · PDBe 5FC6 · UniProt P70158