NADH-quinone oxidoreductase subunit 3 (nqo3) is a 783-residue protein from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q56223.
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The mean pLDDT of this model is 92.7 (very high overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 85% |
| 70 to 90 | Confident: backbone generally right | 12% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is menaquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient required for the synthesis of ATP
NDH-1 is composed of 15 different subunits, Nqo1 to Nqo15. The complex has a L-shaped structure, with the hydrophobic arm (subunits Nqo7, Nqo8 and Nqo10 to Nqo14) embedded in the membrane and the hydrophilic peripheral arm (subunits Nqo1 to Nqo6, Nqo9 and Nqo15) protruding into the bacterial cytoplasm. The hydrophilic domain contains all the redox centers
Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3I9V | X-ray | 3.1 Å | 3/C=1-783 |
| 3IAM | X-ray | 3.1 Å | 3/C=1-783 |
| 6Y11 | X-ray | 3.11 Å | 3/D=1-783 |
| 3IAS | X-ray | 3.15 Å | 3/C/L/U=1-783 |
| 6I1P | X-ray | 3.21 Å | 3/D=1-783 |
| 2FUG | X-ray | 3.3 Å | 3/C/L/U=1-783 |
| 4HEA | X-ray | 3.3 Å | 3/D=1-783 |
| 6Q8W | X-ray | 3.4 Å | 3/D=1-783 |
| 6Q8X | X-ray | 3.51 Å | 3/D=1-783 |
| 6I0D | X-ray | 3.6 Å | 3/D=1-783 |
| 6Q8O | X-ray | 3.6 Å | 3/D=1-783 |
| 6ZIY | EM | 4.25 Å | 3=1-783 |
| 6ZJL | EM | 4.3 Å | 3=1-783 |
| 3M9S | X-ray | 4.5 Å | 3/C=1-783 |
| 6ZJY | EM | 5.5 Å | 3=1-783 |
| 6ZJN | EM | 6.1 Å | 3=1-783 |
| 2YBB | EM | 19.0 Å | 3=1-783 |
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