Crystal structure of recombinant human beta-glucocerebrosidase in complex with cyclophellitol activity based probe with CY5 tag (ME569)

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).

Ligands and binding sites

• HKW · 6-[3,3-dimethyl-2-[(1~{E},3~{E},5~{E})-5-(1,3,3-trimethylindol-2-ylidene)penta-1,3-dienyl]indol-1-ium-1-yl]-~{N}-[[1-[[(1~{S},2~{R},3~{R},4~{S},6~{S})-2,3, 4,6-tetrakis(oxidanyl)cyclohexyl]methyl]-1,2,3-triazol-4-yl]methyl]hexanamide · ligand · 2 copies · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
• SO4 · Sulfate ion · ion · 27 copies · chains A, B
• ACT · Acetate ion · additive · 20 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 443 Ų buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide, 3 glycan, 2 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 6Q6K · Crystal structure of recombinant human beta-glucocerebrosidase in complex with… · the same entry in another collection · chain B against B, TM-score 1.00
• P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · a predicted model of the same protein · chain B 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 P04062
• Elsewhere: RCSB PDB 6Q6K · PDBe 6Q6K · UniProt P04062