Research workbench
Structure of the NDI1 protein from saccharomyces cerevisiae in complex with AC0-12.
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
- 5YJY
- 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, 8WF, MG
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 463 | 32% helix, 23% strand | P32340 |
| B | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial (EC 1.6.5.9) | protein | 465 | 33% helix, 21% strand | P32340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- 8WF · 2-dodecyl-1-oxidanidyl-quinolin-1-ium-4-ol · 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
10 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.79 | 0.82 | 78 | FAD, MG, 8WF, MES |
| 2 | 979 | 0.79 | 0.80 | 89 | FAD, MG, 8WF, MES |
| 3 | 428 | 0.78 | 0.87 | 53 | empty |
| 4 | 114 | 0.78 | 0.97 | 28 | empty |
| 5 | 405 | 0.75 | 0.85 | 51 | empty |
Interfaces
1 interface between chains.
- A–B · 1634 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5YJY · Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with AC0-12. · 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 5YJY · PDBe 5YJY · UniProt P32340
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