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Structural studies of a glycoside hydrolase family 3 beta-glucosidase from the model fungus neurospora crassa
Analyse Structural studies of a glycoside hydrolase family 3 beta-glucosidase from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NBS
- Type
- protein
- Length
- 1,683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q7RWP2
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 842 | 26% helix, 20% strand | Q7RWP2 |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 841 | 26% helix, 19% strand | Q7RWP2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 36 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 11 copies · chains A, 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 | 65 | 0.72 | 0.98 | 35 | empty |
| 2 | 164 | 0.70 | 0.89 | 32 | empty |
| 3 | 171 | 0.69 | 0.88 | 37 | empty |
| 4 | 367 | 0.67 | 0.81 | 53 | empty |
| 5 | 227 | 0.61 | 0.81 | 36 | NAG |
Interfaces
1 interface between chains.
- A–B · 1683 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5NBS · Structural studies of a Glycoside Hydrolase Family 3 beta-glucosidase from the Model… · the same entry in another collection · chain B against B, 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 Q7RWP2
- Elsewhere: RCSB PDB 5NBS · PDBe 5NBS · UniProt Q7RWP2
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