MolNFT v2 · #120374 · protein
The E171Q mutant structure of Bgl6
5GNX · Beta-glucosidase: “The E171Q mutant structure of Bgl6”. X-ray diffraction at 1.8, 1 ligand (BGC), 8 pockets (best druggability 0.69). MolNFT v2 #120374 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GNX
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- metagenome
- Molecule
- Beta-glucosidase
- EC
- 3.2.1.21
- Ligands
- BGC
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.8 · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-glucosidase (EC 3.2.1.21) | protein | 451 | 43% helix, 15% strand | — |
| B | Beta-glucosidase (EC 3.2.1.21) | protein | 449 | 44% helix, 15% strand | — |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- PPI · Propanoic acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.69 | 0.79 | 50 | BGC |
| 2 | 502 | 0.69 | 0.79 | 52 | BGC |
| 3 | 109 | 0.54 | 0.84 | 30 | empty |
| 4 | 147 | 0.45 | 0.77 | 19 | PPI |
| 5 | 147 | 0.44 | 0.76 | 22 | PPI |
Interfaces
1 interface between chains.
- A–B · 1039 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 glycan (glycosylation).
Compared structures
- 5GNX · The E171Q mutant structure of BGL6 · the same entry in another collection · 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
- Elsewhere: RCSB PDB 5GNX · PDBe 5GNX
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