MolNFT v1 · #51303 · protein
Acid-beta-glucosidase with N-butyl-deoxynojirimycin
2V3D · Glucosylceramidase: “Acid-beta-glucosidase with N-butyl-deoxynojirimycin”. X-ray diffraction, 5 ligands (NBV, NAG, BMA), 9 pockets (best druggability 0.86). MolNFT v1 #51303 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2V3D
- Type
- protein
- Length
- 992 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
- NBV, NAG, BMA, FUC, SO4
- Pockets
- 9 · 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 | 495 | 28% helix, 28% strand | P04062 |
| B | Glucosylceramidase (EC 3.2.1.45) | protein | 497 | 28% helix, 28% strand | P04062 |
Ligands and binding sites
- NBV · (2R,3R,4R,5S)-1-butyl-2-(hydroxymethyl)piperidine-3,4,5-triol · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.86 | 0.91 | 52 | NBV |
| 2 | 512 | 0.68 | 0.79 | 63 | SO4 |
| 3 | 377 | 0.67 | 0.80 | 37 | SO4 |
| 4 | 211 | 0.63 | 0.83 | 28 | empty |
| 5 | 328 | 0.63 | 0.79 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1030 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 2V3D · PDBe 2V3D · UniProt P04062
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