MolNFT v1 · #118071 · protein
Water-forming NADH oxidase from lactobacillus brevis (lbnox)
5ER0: “Water-forming NADH oxidase from lactobacillus brevis (lbnox)”. X-ray diffraction, 2 ligands (FAD, OXY), 11 pockets (best druggability 0.88). MolNFT v1 #118071 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ER0
- Type
- protein
- Length
- 1,800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH oxidase
- UniProt
- M5B0V2
- Ligands
- FAD, OXY
- Pockets
- 11 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADH oxidase | protein | 450 | 28% helix, 30% strand | M5B0V2 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- OXY · Oxygen molecule · ion · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.88 | 0.91 | 115 | FAD, OXY |
| 2 | 584 | 0.87 | 0.92 | 91 | FAD, OXY |
| 3 | 416 | 0.83 | 0.91 | 61 | FAD, OXY, EDO |
| 4 | 841 | 0.83 | 0.85 | 95 | FAD, OXY, EDO |
| 5 | 469 | 0.69 | 0.79 | 52 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2802 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2792 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 787 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5ER0 · Water-forming NADH oxidase from Lactobacillus brevis (LbNOX) · 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 5ER0 · PDBe 5ER0 · UniProt M5B0V2
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