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X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide
Analyse X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y7V
- 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
- INS, NAG, SO4
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 27% helix, 29% strand | P04062 |
Ligands and binding sites
- INS · 1,2,3,4,5,6-hexahydroxy-cyclohexane · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 13 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.64 | 0.79 | 52 | empty |
| 2 | 186 | 0.56 | 0.80 | 34 | SO4 |
| 3 | 121 | 0.47 | 0.78 | 21 | INS |
| 4 | 124 | 0.46 | 0.78 | 20 | INS |
| 5 | 98 | 0.37 | 0.75 | 16 | SO4 |
Interfaces
1 interface between chains.
- A–B · 376 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 1Y7V · X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide · 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 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 1Y7V · PDBe 1Y7V · UniProt P04062
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