MolNFT v1 · #21056 · protein
Crystal structure of the shifted form of the glucose-fructose oxidoreductase from zymomonas mobilis
1RYE: “Crystal structure of the shifted form of the glucose-fructose oxidoreductase from zymomonas mobilis”. X-ray diffraction, 1 ligand (NDP), 19 pockets (best druggability 0.84). MolNFT v1 #21056 on GenesisL1: 3D structure, binding sites…
- PDB
- 1RYE
- Type
- protein
- Length
- 1,423 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-fructose oxidoreductase
- EC
- 1.1.99.28
- UniProt
- Q07982
- Ligands
- NDP
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 343 | 40% helix, 23% strand | Q07982 |
| B | Glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 371 | 36% helix, 23% strand | Q07982 |
| C | Glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 339 | 40% helix, 24% strand | Q07982 |
| D | Glucose-fructose oxidoreductase (EC 1.1.99.28) | protein | 370 | 38% helix, 22% strand | Q07982 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, D
- BME · Beta-mercaptoethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1084 | 0.84 | 0.85 | 105 | NDP |
| 2 | 1020 | 0.83 | 0.84 | 100 | NDP |
| 3 | 440 | 0.70 | 0.81 | 44 | NDP, GOL |
| 4 | 105 | 0.69 | 0.92 | 22 | empty |
| 5 | 448 | 0.66 | 0.79 | 47 | NDP |
Interfaces
5 interfaces between chains.
- A–B · 1718 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 1660 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 1572 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1429 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 625 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1RYE · Crystal Structure of the Shifted Form of the Glucose-Fructose Oxidoreductase from… · the same entry in another collection · chain D against D, TM-score 1.00
- Q07982 · AlphaFold monomer V2.0 prediction for glucose--fructose oxidoreductase (Q07982) · a predicted model of the same protein · chain C 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 Q07982
- Elsewhere: RCSB PDB 1RYE · PDBe 1RYE · UniProt Q07982
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