Research workbench
The acid beta-glucosidase active site exhibits plasticity in binding 3,4,5,6-tetrahydroxyazepane-based inhibitors: implications for pharmacological chaperone design for gaucher disease
Analyse The acid beta-glucosidase active site exhibits plasticity in binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RIL
- Type
- protein
- Length
- 1,986 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- P04062
- Ligands
- 3RK, NAG, SO4
- Pockets
- 16 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glucosylceramidase (EC 3.2.1.45) | protein | 496 | 27% helix, 29% strand | P04062 |
| B, D | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 27% helix, 28% strand | P04062 |
Ligands and binding sites
- 3RK · (3S,4R,5R,6S)-azepane-3,4,5,6-tetrol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 36 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 854 | 0.84 | 0.87 | 87 | SO4 |
| 2 | 1139 | 0.81 | 0.82 | 91 | 3RK |
| 3 | 526 | 0.78 | 0.85 | 59 | 3RK |
| 4 | 452 | 0.67 | 0.79 | 50 | empty |
| 5 | 324 | 0.66 | 0.81 | 43 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1046 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1030 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 677 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 668 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 184 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3RIL · The acid beta-glucosidase active site exhibits plasticity in binding… · the same entry in another collection · chain D against D, 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 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 3RIL · PDBe 3RIL · UniProt P04062
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