MolNFT v1 · #74223 · protein
Crystal structure of putative oxidoreductase from bradyrhizobium japonicum usda 110
3OQB: “Crystal structure of putative oxidoreductase from bradyrhizobium japonicum usda 110”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT v1 #74223 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OQB
- Type
- protein
- Length
- 3,017 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase
- UniProt
- Q89RD2
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 6 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxidoreductase | protein | 376 | 35% helix, 25% strand | Q89RD2 |
| B, E | Oxidoreductase | protein | 377 | 35% helix, 25% strand | Q89RD2 |
| C | Oxidoreductase | protein | 377 | 36% helix, 26% strand | Q89RD2 |
| D, G | Oxidoreductase | protein | 378 | 37% helix, 25% strand | Q89RD2 |
| F | Oxidoreductase | protein | 379 | 36% helix, 24% strand | Q89RD2 |
| H | Oxidoreductase | protein | 375 | 35% helix, 25% strand | Q89RD2 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.82 | 0.98 | 27 | empty |
| 2 | 144 | 0.82 | 0.98 | 26 | empty |
| 3 | 160 | 0.81 | 0.97 | 26 | empty |
| 4 | 158 | 0.81 | 0.97 | 25 | empty |
| 5 | 609 | 0.78 | 0.84 | 56 | empty |
Interfaces
16 interfaces between chains.
- D–E · 3582 Ų buried · 49 hydrogen bonds · protein-protein
- B–H · 3501 Ų buried · 43 hydrogen bonds · protein-protein
- A–G · 3487 Ų buried · 44 hydrogen bonds · protein-protein
- C–F · 3481 Ų buried · 39 hydrogen bonds · protein-protein
- D–H · 751 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 64 modified (engineered).
Compared structures
- 3OQB · CRYSTAL STRUCTURE OF putative oxidoreductase from Bradyrhizobium japonicum USDA 110 · 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 Q89RD2
- Elsewhere: RCSB PDB 3OQB · PDBe 3OQB · UniProt Q89RD2
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