MolNFT v1 · #11043 · protein
Structure of coenzyme F420H2:NADP+ oxidoreductase (fno) with its substrates bound
1JAY: “Structure of coenzyme F420H2:NADP+ oxidoreductase (fno) with its substrates bound”. X-ray diffraction, 3 ligands (NAP, F42, NA), 4 pockets (best druggability 0.58). MolNFT v1 #11043 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JAY
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coenzyme F420H2:NADP+ oxidoreductase (fno)
- UniProt
- O29370
- Ligands
- NAP, F42, NA
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Coenzyme F420H2:NADP+ oxidoreductase (fno) | protein | 212 | 44% helix, 23% strand | O29370 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- F42 · Coenzyme F420 · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.58 | 0.77 | 28 | NAP |
| 2 | 288 | 0.57 | 0.77 | 27 | NAP |
| 3 | 68 | 0.32 | 0.76 | 15 | empty |
| 4 | 60 | 0.32 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1425 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 1JAY · Structure of Coenzyme F420H2:NADP+ Oxidoreductase (FNO) with its substrates bound · the same entry in another collection · chain A against A, TM-score 1.00
- O29370 · AlphaFold monomer V2.0 prediction for F420-dependent NADP reductase (O29370) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O29370
- Elsewhere: RCSB PDB 1JAY · PDBe 1JAY · UniProt O29370
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