Research workbench
Structure of the NDI1 protein from saccharomyces cerevisiae in complex with myxothiazol.
Analyse Structure of the NDI1 protein from saccharomyces cerevisiae in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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