The extracellular region of CD33 with bound sialoside analogue P22

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 45% strand (DSSP).

Ligands and binding sites

• FVP · 2-aminoethyl 5-{[(4-cyclohexyl-1H-1,2,3-triazol-1-yl) acetyl]amino}-3,5,9-trideoxy-9-[(4-hydroxy-3,5-dimethylbenzene-1-carbonyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranonosyl-(2->6)-beta-D-galactopyranosyl-(1->4)-beta-D-glucopyranoside · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B
• PO4 · Phosphate ion · ion · chains B
• EDO · 1,2-ethanediol · additive · 2 copies · chains 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, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 846 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).

Compared structures

• 7AW6 · The extracellular region of CD33 with bound sialoside analogue P22 · the same entry in another collection · chain A against A, TM-score 1.00
• P20138 · AlphaFold monomer V2.0 prediction for myeloid cell surface antigen CD33 (P20138) · 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 P20138
• Elsewhere: RCSB PDB 7AW6 · PDBe 7AW6 · UniProt P20138