Research workbench
Crystal structure of glucose dehydrogenase
Analyse Crystal structure of glucose dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CDY
- Type
- protein
- Length
- 690 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose dehydrogenase
- Ligands
- CA
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose dehydrogenase | protein | 346 | 4% helix, 44% strand | — |
| B | Glucose dehydrogenase | protein | 344 | 4% helix, 44% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.70 | 0.77 | 55 | empty |
| 2 | 443 | 0.64 | 0.77 | 29 | empty |
| 3 | 298 | 0.59 | 0.78 | 35 | GOL |
| 4 | 80 | 0.35 | 0.75 | 16 | empty |
| 5 | 109 | 0.34 | 0.73 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7CDY · Crystal structure of glucose dehydrogenase · 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 7CDY · PDBe 7CDY
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