Research workbench
Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete Phanerochaete chrysosporium in complex with gluconolactone
Analyse Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2E40
- Type
- protein
- Length
- 918 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Phanerochaete chrysosporium
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- UniProt
- Q25BW5
- Ligands
- LGC
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · resolution 1.9 · 1 distinct chain · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Beta-glucosidase (EC 3.2.1.21) | protein | 459 | 47% helix, 17% strand | Q25BW5 |
Ligands and binding sites
- LGC · D-glucono-1,5-lactone · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.72 | 0.82 | 39 | LGC |
| 2 | 373 | 0.72 | 0.83 | 40 | LGC |
| 3 | 329 | 0.57 | 0.76 | 32 | empty |
| 4 | 254 | 0.53 | 0.76 | 25 | empty |
| 5 | 242 | 0.52 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2E40 · Crystal structure of intracellular family 1 beta-glucosidase BGL1A from the basidiomycete… · the same entry in another collection · chain A against A, TM-score 1.00
- Q25BW5 · AlphaFold monomer V2.0 prediction for beta-glucosidase 1A (Q25BW5) · 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 Q25BW5
- Elsewhere: RCSB PDB 2E40 · PDBe 2E40 · UniProt Q25BW5
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