MolNFT v1 · #46053 · protein
Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into gaucher disease
2NSX · Glucosylceramidase: “Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into gaucher disease”. X-ray diffraction, 3 ligands (IFM, NAG, SO4), 19 pockets (best druggability 0.85). MolNFT v1 #46053 on…
- PDB
- 2NSX
- Type
- protein
- Length
- 1,988 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
- IFM, NAG, SO4
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 27% helix, 29% strand | P04062 |
Ligands and binding sites
- IFM · 5-hydroxymethyl-3,4-dihydroxypiperidine · ligand · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 18 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.85 | 0.89 | 61 | GOL, IFM |
| 2 | 676 | 0.85 | 0.88 | 70 | GOL, IFM |
| 3 | 834 | 0.84 | 0.87 | 107 | SO4 |
| 4 | 460 | 0.69 | 0.80 | 46 | empty |
| 5 | 371 | 0.69 | 0.82 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–D · 976 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 959 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 740 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 188 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 2NSX · Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into… · 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 2NSX · PDBe 2NSX · UniProt P04062
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