MolNFT v1 · #157118 · protein
Structure of acid-beta-glucosidase in complex with an aromatic pyrrolidine iminosugar inhibitor
6MOZ · Glucosylceramidase: “Structure of acid-beta-glucosidase in complex with an aromatic pyrrolidine iminosugar inhibitor”. X-ray diffraction, 4 ligands (JXA, NAG, NA), 7 pockets (best druggability 0.82). MolNFT v1 #157118 on GenesisL1…
- PDB
- 6MOZ
- Type
- protein
- Length
- 994 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- P04062
- Ligands
- JXA, NAG, NA, PO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 27% helix, 28% strand | P04062 |
Ligands and binding sites
- JXA · (2R,3S,4R)-2-{[4-(3,5-dichlorophenyl)-1H-1,2,3-triazol-1-yl]methyl}pyrrolidine-3,4-diol · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 32 copies · chains A, B
- PO4 · Phosphate ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.82 | 0.83 | 87 | JXA, NA, GOL |
| 2 | 145 | 0.50 | 0.79 | 23 | NA |
| 3 | 139 | 0.49 | 0.78 | 34 | empty |
| 4 | 98 | 0.44 | 0.79 | 25 | empty |
| 5 | 92 | 0.43 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 521 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6MOZ · Structure of acid-beta-glucosidase in complex with an aromatic pyrrolidine iminosugar… · the same entry in another collection · chain A against A, TM-score 1.00
- P04062 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (P04062) · 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 P04062
- Elsewhere: RCSB PDB 6MOZ · PDBe 6MOZ · UniProt P04062
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