MolNFT v1 · #33223 · protein
The crystal structure of water-forming NAD(P)H oxidase from lactobacillus sanfranciscensis
2CDU · NADPH oxidase: “The crystal structure of water-forming NAD(P)H oxidase from lactobacillus sanfranciscensis”. X-ray diffraction, 2 ligands (FAD, ADP), 6 pockets (best druggability 0.83). MolNFT v1 #33223 on GenesisL1: 3D structure…
- PDB
- 2CDU
- Type
- protein
- Length
- 900 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH oxidase
- EC
- 1.6.-.-
- UniProt
- Q9F1X5
- Ligands
- FAD, ADP
- Pockets
- 6 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH oxidase (EC 1.6.-.-) | protein | 451 | 29% helix, 31% strand | Q9F1X5 |
| B | NADPH oxidase (EC 1.6.-.-) | protein | 449 | 30% helix, 31% strand | Q9F1X5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.83 | 0.84 | 102 | FAD, ADP |
| 2 | 1118 | 0.83 | 0.83 | 100 | FAD, ADP |
| 3 | 245 | 0.54 | 0.76 | 24 | empty |
| 4 | 214 | 0.54 | 0.77 | 23 | empty |
| 5 | 72 | 0.45 | 0.82 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 3109 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 2CDU · The Crystal Structure of Water-forming NAD(P)H Oxidase from Lactobacillus sanfranciscensis · 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 Q9F1X5
- Elsewhere: RCSB PDB 2CDU · PDBe 2CDU · UniProt Q9F1X5
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