MolNFT v1 · #92490 · protein
Structure of the NDI1 protein from saccharomyces cerevisiae
4G9K · Rotenone-insensitive NADH-ubiquinone oxidoreductase: “Structure of the NDI1 protein from saccharomyces cerevisiae”. X-ray diffraction, 1 ligand (FAD), 10 pockets (best druggability 0.80). MolNFT v1 #92490 on GenesisL1: 3D structure…
- PDB
- 4G9K
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rotenone-insensitive NADH-ubiquinone oxidoreductase
- EC
- 1.6.5.9
- UniProt
- P32340
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rotenone-insensitive NADH-ubiquinone oxidoreductase (EC 1.6.5.9) | protein | 463 | 36% helix, 26% strand | P32340 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.80 | 0.81 | 94 | FAD |
| 2 | 1105 | 0.80 | 0.81 | 108 | FAD |
| 3 | 413 | 0.79 | 0.87 | 44 | empty |
| 4 | 519 | 0.78 | 0.85 | 54 | empty |
| 5 | 87 | 0.73 | 0.96 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1977 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4G9K · Structure of the Ndi1 protein from Saccharomyces cerevisiae · 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 1.00
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 4G9K · PDBe 4G9K · UniProt P32340
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