Research workbench
X-ray structure of acid-beta-glucosidase with 5N,6O-(N'-(N-octyl) IMINO)NOJIRIMYCIN in the active site
Analyse X-ray structure of acid-beta-glucosidase with 5N,6O-(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
- 2XWD
- Type
- protein
- Length
- 985 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
- LGS, NAG, FUC, MAN, BMA, SO4
- Pockets
- 6 · best druggability 0.83
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 | 493 | 28% helix, 28% strand | P04062 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 492 | 27% helix, 27% strand | P04062 |
Ligands and binding sites
- LGS · (3Z,5S,6R,7S,8R,8aR)-3-(octylimino)hexahydro[1,3]oxazolo[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
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 10 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.83 | 0.84 | 80 | LGS |
| 2 | 485 | 0.67 | 0.78 | 55 | empty |
| 3 | 203 | 0.65 | 0.84 | 28 | empty |
| 4 | 115 | 0.60 | 0.86 | 26 | empty |
| 5 | 66 | 0.29 | 0.73 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 903 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2XWD · X-ray structure of acid-beta-glucosidase with 5N,6O-(N'-(N-OCTYL)IMINO)NOJIRIMYCIN in the… · 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 2XWD · PDBe 2XWD · UniProt P04062
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