MolNFT v1 · #127641 · protein
F420:NADPH oxidoreductase from thermobifida fusca with NADP+ bound
5N2I · Reduced coenzyme F420:NADP oxidoreductase: “F420:NADPH oxidoreductase from thermobifida fusca with NADP+ bound”. X-ray diffraction, 1 ligand (NAP), 7 pockets (best druggability 0.79). MolNFT v1 #127641 on GenesisL1: 3D structure…
- PDB
- 5N2I
- Type
- protein
- Length
- 893 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Reduced coenzyme F420:NADP oxidoreductase
- EC
- 1.6.99.-
- UniProt
- Q47RA9
- Ligands
- NAP
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Reduced coenzyme F420:NADP oxidoreductase (EC 1.6.99.-) | protein | 225 | 38% helix, 23% strand | Q47RA9 |
| B, C | Reduced coenzyme F420:NADP oxidoreductase (EC 1.6.99.-) | protein | 223 | 39% helix, 23% strand | Q47RA9 |
| D | Reduced coenzyme F420:NADP oxidoreductase (EC 1.6.99.-) | protein | 222 | 38% helix, 23% strand | Q47RA9 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, C, B, D
- GOL · Glycerol · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 484 | 0.79 | 0.86 | 44 | NAP |
| 2 | 467 | 0.78 | 0.86 | 40 | NAP, GOL |
| 3 | 221 | 0.50 | 0.75 | 28 | NAP, GOL |
| 4 | 232 | 0.50 | 0.75 | 28 | NAP, GOL |
| 5 | 135 | 0.41 | 0.75 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1879 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1842 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 963 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 37 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 35 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5N2I · F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound · 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 Q47RA9
- Elsewhere: RCSB PDB 5N2I · PDBe 5N2I · UniProt Q47RA9
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