Research workbench
Cooperative effect of two surface amino acid mutations (Q252L and E170K) of glucose dehydrogenase from bacillus megaterium IWG3 for the stabilization of oligomeric state
Analyse Cooperative effect of two surface amino acid mutations (Q252L and E170K) of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RWB
- Type
- protein
- Length
- 1,044 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
- P40288
- Ligands
- NAD
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Glucose 1-dehydrogenase (EC 1.1.1.47) | protein | 261 | 54% helix, 15% strand | P40288 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.75 | 0.82 | 59 | NAD |
| 2 | 592 | 0.74 | 0.81 | 59 | NAD |
| 3 | 657 | 0.74 | 0.80 | 59 | NAD |
| 4 | 573 | 0.74 | 0.81 | 60 | NAD |
| 5 | 406 | 0.69 | 0.81 | 43 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1604 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1586 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 294 Ų buried · 2 hydrogen bonds · protein-protein
- B–F · 89 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1RWB · Cooperative Effect of Two Surface Amino Acid Mutations (Q252L and E170K) of Glucose… · the same entry in another collection · chain F against F, TM-score 1.00
- P40288 · AlphaFold monomer V2.0 prediction for glucose 1-dehydrogenase (P40288) · a predicted model of the same protein · chain B 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 P40288
- Elsewhere: RCSB PDB 1RWB · PDBe 1RWB · UniProt P40288
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