Research workbench
X-ray structure of a conjugate with conduritol-beta-epoxide of acid- beta-glucosidase overexpressed in cultured plant cells
Analyse X-ray structure of a conjugate with conduritol-beta-epoxide of acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VT0
- Type
- protein
- Length
- 983 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosylceramidase
- EC
- 3.2.1.45
- UniProt
- Q9BDT0
- Ligands
- CBU, NAG, FUC, MAN, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosylceramidase (EC 3.2.1.45) | protein | 494 | 28% helix, 27% strand | Q9BDT0 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 489 | 28% helix, 28% strand | Q9BDT0 |
Ligands and binding sites
- CBU · (1R,2R,3S,4S,5S,6S)-cyclohexane-1,2,3,4,5,6-hexol · 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
- 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
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 677 | 0.86 | 0.90 | 53 | CBU |
| 2 | 479 | 0.68 | 0.79 | 47 | SO4 |
| 3 | 448 | 0.67 | 0.79 | 45 | SO4 |
| 4 | 200 | 0.66 | 0.85 | 26 | empty |
| 5 | 58 | 0.39 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 2VT0 · X-ray structure of a conjugate with conduritol-beta-epoxide of acid-beta-glucosidase… · the same entry in another collection · chain B against B, TM-score 1.00
- Q9BDT0 · AlphaFold monomer V2.0 prediction for lysosomal acid glucosylceramidase (Q9BDT0) · 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 Q9BDT0
- Elsewhere: RCSB PDB 2VT0 · PDBe 2VT0 · UniProt Q9BDT0
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