Research workbench
X-ray structure of acid-beta-glucosidase with 5N,6S-(N'-(N-octyl) imino)-6-thionojirimycin in the active site
Analyse X-ray structure of acid-beta-glucosidase with 5N,6S-(N'-(N-octyl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XWE
- 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
- AMF, NAG, BMA, FUC, K, PO4
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 496 | 27% helix, 27% strand | P04062 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 498 | 27% helix, 28% strand | P04062 |
Ligands and binding sites
- AMF · (3Z,5S,6R,7S,8R,8aS)-3-(octylimino)hexahydro[1,3]thiazolo[3,4-a]pyridine-5,6,7,8-tetrol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.84 | 0.85 | 73 | AMF |
| 2 | 185 | 0.70 | 0.88 | 36 | empty |
| 3 | 380 | 0.67 | 0.80 | 44 | empty |
| 4 | 174 | 0.63 | 0.84 | 24 | empty |
| 5 | 241 | 0.54 | 0.77 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 902 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2XWE · X-ray structure of acid-beta-glucosidase with 5N,6S-(N'-(N-OCTYL)IMINO)-6-thionojirimycin… · 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 2XWE · PDBe 2XWE · UniProt P04062
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