Research workbench
Crystal structure of a 6-phospho-beta-glucosidase from bacillus licheniformis
Analyse Crystal structure of a 6-phospho-beta-glucosidase from bacillus licheniformis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WGD
- Type
- protein
- Length
- 1,358 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-glucosidase
- EC
- 3.2.1.86
- UniProt
- A0A5Q3BW14
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 436 | 43% helix, 14% strand | A0A5Q3BW14 |
| B | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 465 | 41% helix, 15% strand | A0A5Q3BW14 |
| C | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 457 | 43% helix, 15% strand | A0A5Q3BW14 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C
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 | 741 | 0.76 | 0.81 | 79 | empty |
| 2 | 352 | 0.70 | 0.82 | 39 | empty |
| 3 | 338 | 0.60 | 0.77 | 37 | empty |
| 4 | 114 | 0.46 | 0.78 | 20 | empty |
| 5 | 78 | 0.43 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 753 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6WGD · Crystal structure of a 6-phospho-beta-glucosidase from Bacillus licheniformis · 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
- Every structure of UniProt A0A5Q3BW14
- Elsewhere: RCSB PDB 6WGD · PDBe 6WGD · UniProt A0A5Q3BW14
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