MolNFT v1 · #123183 · protein
NADP(H) bound NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) from pyrococcus furiosus
5JCA · NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni)…: “NADP(H) bound NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) from pyrococcus furiosus”. X-ray diffraction, 5 ligands (SF4, FAD, NDP), 8 pockets (best druggability 0.82).…
- PDB
- 5JCA
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) subunit alpha; NADH-dependent…
- EC
- 1.6.1.4
- UniProt
- Q8U195, Q8U194
- Ligands
- SF4, FAD, NDP, FES, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) subunit alpha (EC 1.6.1.4) | protein | 471 | 40% helix, 19% strand | Q8U195 |
| S | NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) subunit beta (EC 1.6.1.4) | protein | 279 | 32% helix, 32% strand | Q8U194 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains L
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains L, S
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains L
- FES · Fe2/s2 (inorganic) cluster · ligand · chains S
- MG · Magnesium ion · metal · chains S
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.82 | 0.85 | 100 | FAD, NDP |
| 2 | 741 | 0.79 | 0.83 | 66 | FAD, MG |
| 3 | 110 | 0.49 | 0.80 | 24 | empty |
| 4 | 150 | 0.44 | 0.75 | 22 | empty |
| 5 | 95 | 0.41 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- L–S · 2091 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5JCA · NADP(H) bound NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus… · the same entry in another collection · chain L against L, TM-score 1.00
- Q8U195 · AlphaFold monomer V2.0 prediction for sulfide dehydrogenase subunit alpha (Q8U195) · a predicted model of the same protein · chain L against A, TM-score 0.99
- Q8U194 · AlphaFold monomer V2.0 prediction for sulfide dehydrogenase subunit beta (Q8U194) · a predicted model of the same protein · chain S 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 Q8U195
- Every structure of UniProt Q8U194
- Elsewhere: RCSB PDB 5JCA · PDBe 5JCA · UniProt Q8U195 · UniProt Q8U194
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