MolNFT v1 · #83440 · protein
Structure of a glucose dehydrogenase T277F mutant in complex with D- glucose and naadp
3WIE · Glucose 1-dehydrogenase: “Structure of a glucose dehydrogenase T277F mutant in complex with D- glucose and naadp”. X-ray diffraction, 3 ligands (DN4, BGC, ZN), 20 pockets (best druggability 0.78). MolNFT v1 #83440 on GenesisL1: 3D…
- PDB
- 3WIE
- 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
- DN4, BGC, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 30% 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 | 30% helix, 29% strand | Q979W2 |
Ligands and binding sites
- DN4 · [[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(3-carboxypyridin-1-ium-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphate · ligand · 4 copies · chains A, C, B, D
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 333 | 0.78 | 0.89 | 42 | empty |
| 2 | 314 | 0.78 | 0.89 | 41 | empty |
| 3 | 735 | 0.75 | 0.80 | 68 | ZN, DN4, BGC |
| 4 | 702 | 0.74 | 0.80 | 67 | DN4, BGC |
| 5 | 681 | 0.73 | 0.80 | 70 | ZN, DN4, BGC |
Interfaces
6 interfaces between chains.
- B–D · 2194 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2174 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1041 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1039 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WIE · Structure of a glucose dehydrogenase T277F mutant in complex with D-glucose and NAADP · 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 3WIE · PDBe 3WIE · UniProt Q979W2
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