Research workbench
Structure of a glucose dehydrogenase T277F mutant in complex with NADP
Analyse Structure of a glucose dehydrogenase T277F mutant in complex with NADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WID
- Type
- protein
- Length
- 1,438 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.25
- Source
- Thermoplasma volcanium
- Molecule
- Glucose 1-dehydrogenase
- EC
- 1.1.1.47
- UniProt
- Q979W2
- Ligands
- NAP, ZN
- Pockets
- 18 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.25 · 2 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 360 | 30% helix, 29% strand | Q979W2 |
| C | Glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 358 | 29% helix, 29% strand | Q979W2 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- 1PE · Pentaethylene glycol · additive · 8 copies · chains A, B, C, D
- PGO · S-1,2-propanediol · additive · 4 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 826 | 0.86 | 0.89 | 103 | 1PE |
| 2 | 714 | 0.75 | 0.80 | 63 | NAP |
| 3 | 770 | 0.74 | 0.79 | 79 | NAP |
| 4 | 723 | 0.74 | 0.80 | 63 | NAP |
| 5 | 735 | 0.73 | 0.79 | 65 | NAP |
Interfaces
6 interfaces between chains.
- B–D · 2140 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 2131 Ų buried · 37 hydrogen bonds · protein-protein
- A–B · 1074 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1038 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3WID · Structure of a glucose dehydrogenase T277F mutant in complex with NADP · 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 3WID · PDBe 3WID · UniProt Q979W2
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