Research workbench
Structure of a SUBSTRATE/COFACTOR-unbound glucose dehydrogenase
Analyse Structure of a SUBSTRATE/COFACTOR-unbound glucose dehydrogenase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WIC
- Type
- protein
- Length
- 1,440 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose 1-dehydrogenase
- EC
- 1.1.1.47
- UniProt
- Q979W2
- Ligands
- ZN
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 360 | 29% helix, 29% strand | Q979W2 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 8 copies · chains A, B, C, D
- PGO · S-1,2-propanediol · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.79 | 0.88 | 61 | 1PE |
| 2 | 800 | 0.77 | 0.81 | 74 | empty |
| 3 | 195 | 0.74 | 0.90 | 31 | 1PE |
| 4 | 643 | 0.73 | 0.80 | 72 | empty |
| 5 | 623 | 0.73 | 0.80 | 68 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2169 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 2153 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 1032 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1023 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WIC · Structure of a substrate/cofactor-unbound 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
- Every structure of UniProt Q979W2
- Elsewhere: RCSB PDB 3WIC · PDBe 3WIC · UniProt Q979W2
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