MolNFT v1 · #137385 · protein
Water-forming NADH oxidase from lactobacillus brevis (lbnox) bound to NADH.
5VN0 · NAD(FAD)-dependent dehydrogenase: “Water-forming NADH oxidase from lactobacillus brevis (lbnox) bound to NADH.”. X-ray diffraction, 3 ligands (FAD, NAI, OXY), 20 pockets (best druggability 0.86). MolNFT v1 #137385 on GenesisL1: 3D…
- PDB
- 5VN0
- Type
- protein
- Length
- 3,593 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD(FAD)-dependent dehydrogenase
- UniProt
- Q03Q85
- Ligands
- FAD, NAI, OXY
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, H | NAD(FAD)-dependent dehydrogenase | protein | 449 | 27% helix, 30% strand | Q03Q85 |
| B, C, D | NAD(FAD)-dependent dehydrogenase | protein | 450 | 26% helix, 30% strand | Q03Q85 |
| F, G | NAD(FAD)-dependent dehydrogenase | protein | 448 | 27% helix, 30% strand | Q03Q85 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- OXY · Oxygen molecule · ion · 8 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 585 | 0.86 | 0.91 | 87 | FAD, OXY, NAI |
| 2 | 540 | 0.85 | 0.91 | 79 | FAD, OXY, NAI |
| 3 | 500 | 0.85 | 0.91 | 73 | FAD, OXY, NAI |
| 4 | 508 | 0.85 | 0.91 | 78 | FAD, OXY, NAI |
| 5 | 903 | 0.84 | 0.85 | 102 | FAD, OXY, NAI |
Interfaces
11 interfaces between chains.
- A–B · 2817 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2812 Ų buried · 45 hydrogen bonds · protein-protein
- G–H · 2778 Ų buried · 44 hydrogen bonds · protein-protein
- E–F · 2774 Ų buried · 43 hydrogen bonds · protein-protein
- A–E · 681 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5VN0 · Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) bound to NADH. · 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 Q03Q85
- Elsewhere: RCSB PDB 5VN0 · PDBe 5VN0 · UniProt Q03Q85
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