Research workbench
Crystal structure of 6-phospho-beta-glucosidase from lactobacillus plantarum (apo form)
Analyse Crystal structure of 6-phospho-beta-glucosidase from lactobacillus plantarum… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GZE
- Type
- protein
- Length
- 2,842 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-phospho-beta-glucosidase
- EC
- 3.2.1.86
- UniProt
- F9UU25
- Ligands
- CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 479 | 40% helix, 14% strand | F9UU25 |
| B | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 472 | 41% helix, 15% strand | F9UU25 |
| C | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 476 | 41% helix, 14% strand | F9UU25 |
| E | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 467 | 41% helix, 14% strand | F9UU25 |
| F | 6-phospho-beta-glucosidase (EC 3.2.1.86) | protein | 469 | 41% helix, 14% strand | F9UU25 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.85 | 0.98 | 26 | GOL |
| 2 | 201 | 0.84 | 0.98 | 26 | empty |
| 3 | 202 | 0.83 | 0.97 | 26 | CL |
| 4 | 912 | 0.78 | 0.81 | 89 | empty |
| 5 | 1197 | 0.76 | 0.78 | 105 | CL |
Interfaces
6 interfaces between chains.
- E–F · 1638 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1593 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1577 Ų buried · 24 hydrogen bonds · protein-protein
- B–E · 639 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 411 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 76 modified (engineered).
Compared structures
- 4GZE · Crystal structure of 6-phospho-beta-glucosidase from Lactobacillus plantarum (apo form) · 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 F9UU25
- Elsewhere: RCSB PDB 4GZE · PDBe 4GZE · UniProt F9UU25
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