Research workbench
The structure of Gan1D W433A in complex with cellobiose-6-phosphate
Analyse The structure of Gan1D W433A in complex with cellobiose-6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8B81
- Type
- protein
- Length
- 948 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.585
- Source
- Geobacillus stearothermophilus
- Molecule
- Putative 6-phospho-beta-galactobiosidase
- EC
- 3.2.1.85
- UniProt
- W8QF82
- Ligands
- BGC, BG6
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · resolution 1.585 · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative 6-phospho-beta-galactobiosidase (EC 3.2.1.85) | protein | 474 | 41% helix, 17% strand | W8QF82 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- BG6 · 6-O-phosphono-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- IMD · Imidazole · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.85 | 0.87 | 80 | BGC, BG6 |
| 2 | 834 | 0.85 | 0.87 | 69 | BGC, BG6 |
| 3 | 145 | 0.81 | 0.98 | 26 | empty |
| 4 | 96 | 0.45 | 0.79 | 23 | empty |
| 5 | 129 | 0.44 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1609 Ų buried · 29 hydrogen bonds · protein-protein
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 W8QF82
- Elsewhere: RCSB PDB 8B81 · PDBe 8B81 · UniProt W8QF82
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