Crystal structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to trimannoside

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 41% strand (DSSP).

Ligands and binding sites

• M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · 2 copies · chains A, B
• MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
• MN · Manganese (II) ion · metal · 2 copies · chains A, B

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 · 1108 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 2RL9 · Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to… · the same entry in another collection · chain A against A, TM-score 1.00
• P11456 · AlphaFold monomer V2.0 prediction for cation-dependent mannose-6-phosphate receptor… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P11456
• Elsewhere: RCSB PDB 2RL9 · PDBe 2RL9 · UniProt P11456