MolNFT v1 · #95171 · protein
Crystal structure of beta-glucosidase 1 from aspergillus aculeatus in complex with 1-deoxynojirimycin
4IID: “Crystal structure of beta-glucosidase 1 from aspergillus aculeatus in complex with 1-deoxynojirimycin”. X-ray diffraction, 4 ligands (NOJ, MAN, NAG), 20 pockets (best druggability 0.71). MolNFT v1 #95171 on GenesisL1: 3D structure…
- PDB
- 4IID
- Type
- protein
- Length
- 1,666 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase 1
- EC
- 3.2.1.21
- UniProt
- P48825
- Ligands
- NOJ, MAN, NAG, BMA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase 1 (EC 3.2.1.21) | protein | 834 | 26% helix, 20% strand | P48825 |
| B | Beta-glucosidase 1 (EC 3.2.1.21) | protein | 832 | 27% helix, 19% strand | P48825 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 38 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 33 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 3 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.71 | 0.98 | 25 | empty |
| 2 | 51 | 0.70 | 0.98 | 22 | empty |
| 3 | 421 | 0.66 | 0.79 | 61 | MRD, NOJ |
| 4 | 127 | 0.61 | 0.86 | 27 | empty |
| 5 | 233 | 0.59 | 0.80 | 33 | MPD |
Interfaces
1 interface between chains.
- A–B · 1594 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 4IID · Crystal structure of beta-glucosidase 1 from Aspergillus aculeatus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P48825 · AlphaFold monomer V2.0 prediction for beta-glucosidase 1 (P48825) · a predicted model of the same protein · chain A 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 P48825
- Elsewhere: RCSB PDB 4IID · PDBe 4IID · UniProt P48825
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