MolNFT v1 · #137436 · protein
Crystal structure of engineered water-forming NADPH oxidase (tpnox) bound to NADPH. the G159A, D177A, A178R, M179S, P184R mutant of lbnox.
5VOH · NADH oxidase: “Crystal structure of engineered water-forming NADPH oxidase (tpnox) bound to NADPH. the G159A, D177A, A178R…”. X-ray diffraction, 4 ligands (FAD, NDP, CL), 13 pockets (best druggability 0.87). MolNFT v1 #137436 on…
- PDB
- 5VOH
- Type
- protein
- Length
- 1,795 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH oxidase
- UniProt
- M5B0V2
- Ligands
- FAD, NDP, CL, SO4
- Pockets
- 13 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADH oxidase | protein | 448 | 27% helix, 31% strand | M5B0V2 |
| C | NADH oxidase | protein | 449 | 26% helix, 31% strand | M5B0V2 |
| D | NADH oxidase | protein | 450 | 27% helix, 30% strand | M5B0V2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C, D
- SO4 · Sulfate ion · ion · chains A, C
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.87 | 0.91 | 105 | SO4, FAD, NDP |
| 2 | 627 | 0.86 | 0.90 | 96 | FAD, NDP |
| 3 | 1021 | 0.83 | 0.84 | 117 | FAD, NDP |
| 4 | 863 | 0.82 | 0.84 | 96 | FAD, NDP |
| 5 | 96 | 0.60 | 0.87 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2790 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2766 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 766 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 5VOH · Crystal structure of engineered water-forming NADPH oxidase (TPNOX) bound to NADPH. The… · 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 M5B0V2
- Elsewhere: RCSB PDB 5VOH · PDBe 5VOH · UniProt M5B0V2
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