MolNFT v1 · #140723 · protein
Structure of the NDI1 protein from saccharomyces cerevisiae in complex with myxothiazol.
5YJX · Rotenone-insensitive NADH-ubiquinone oxidoreductase…: “Structure of the NDI1 protein from saccharomyces cerevisiae in complex with myxothiazol.”. X-ray diffraction, 3 ligands (FAD, MYX, MG), 11 pockets (best druggability 0.79).…
- PDB
- 5YJX
- Type
- protein
- Length
- 928 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
- EC
- 1.6.5.9
- UniProt
- P32340
- Ligands
- FAD, MYX, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 464 | 35% helix, 21% strand | P32340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- MYX · (2Z,6E)-7-{2'-[(2E,4E)-1,6-dimethylhepta-2,4-dienyl]-2, 4'-bi-1,3-thiazol-4-yl}-3,5-dimethoxy-4-methylhepta-2, 6-dienamide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 8 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.79 | 0.81 | 80 | FAD, MG, MES, MYX |
| 2 | 1117 | 0.79 | 0.80 | 98 | FAD, MG, MES, MYX |
| 3 | 379 | 0.79 | 0.88 | 49 | empty |
| 4 | 399 | 0.76 | 0.85 | 47 | empty |
| 5 | 91 | 0.75 | 0.97 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1849 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5YJX · Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol. · the same entry in another collection · chain A against A, TM-score 1.00
- P32340 · AlphaFold monomer V2.0 prediction for rotenone-insensitive NADH- ubiquinone… · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P32340
- Elsewhere: RCSB PDB 5YJX · PDBe 5YJX · UniProt P32340
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