MolNFT v1 · #123285 · protein
NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) from pyrococcus furiosus
5JFC · NADH-dependent FERREDOXIN:NADP oxidoreductase subunit alpha: “NADH-dependent FERREDOXIN:NADP oxidoreductase (nfni) from pyrococcus furiosus”. X-ray diffraction, 4 ligands (SF4, FAD, FES), 10 pockets (best druggability 0.82). MolNFT…
- PDB
- 5JFC
- Type
- protein
- Length
- 742 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADH-dependent FERREDOXIN:NADP oxidoreductase subunit alpha; NADH-dependent…
- EC
- 1.6.1.4
- UniProt
- Q8U195, Q8U194
- Ligands
- SF4, FAD, FES, MG
- Pockets
- 10 · 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 subunit alpha (EC 1.6.1.4) | protein | 463 | 41% helix, 17% strand | Q8U195 |
| S | NADH-dependent FERREDOXIN:NADP oxidoreductase 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
- FES · Fe2/s2 (inorganic) cluster · ligand · chains S
- MG · Magnesium ion · metal · chains S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.82 | 0.87 | 89 | FAD |
| 2 | 719 | 0.79 | 0.83 | 67 | FAD, MG |
| 3 | 56 | 0.67 | 0.95 | 16 | empty |
| 4 | 56 | 0.50 | 0.87 | 23 | empty |
| 5 | 155 | 0.46 | 0.77 | 21 | empty |
Interfaces
1 interface between chains.
- L–S · 2085 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5JFC · NADH-dependent Ferredoxin:NADP Oxidoreductase (NfnI) from Pyrococcus furiosus · 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 5JFC · PDBe 5JFC · UniProt Q8U195 · UniProt Q8U194
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