Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' cmp

Structure

x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).

Ligands and binding sites

• C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, C
• RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, A, C
• ZN · Zinc ion · metal · 6 copies · chains A, B, C
• SCN · Thiocyanate ion · ion · 2 copies · chains C
• GOL · Glycerol · additive · 2 copies · chains B
• MLI · Malonate ion · additive · chains B

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

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 497 Ų buried · 3 hydrogen bonds · protein-protein
• A–C · 488 Ų buried · 4 hydrogen bonds · protein-protein
• B–C · 149 Ų buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

• 5EBE · Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' CMP · the same entry in another collection · chain A against A, TM-score 1.00
• Q92484 · AlphaFold monomer V2.0 prediction for acid sphingomyelinase-like phosphodiesterase 3A… · a predicted model of the same protein · chain C 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 Q92484
• Elsewhere: RCSB PDB 5EBE · PDBe 5EBE · UniProt Q92484