Nitrogenase molybdenum-iron protein alpha chain (nifD) is a 492-residue protein from Azotobacter vinelandii. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P07328.
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The mean pLDDT of this model is 97.5 (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 | 97% |
| 70 to 90 | Confident: backbone generally right | 0% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
This molybdenum-iron protein is part of the nitrogenase complex that catalyzes the key enzymatic reactions in nitrogen fixation
Tetramer of two alpha and two beta chains. Forms complex with the iron protein (nitrogenase component 2)
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3U7Q | X-ray | 1.0 Å | A/C=1-492 |
| 1M1N | X-ray | 1.16 Å | A/C/E/G=2-492 |
| 7JRF | X-ray | 1.33 Å | A/C=1-492 |
| 6O7M | X-ray | 1.4 Å | A/C=1-492 |
| 4TKU | X-ray | 1.43 Å | A/C=1-492 |
| 4TKV | X-ray | 1.5 Å | A/C=1-492 |
| 5BVH | X-ray | 1.53 Å | A/C=1-492 |
| 8P8G | X-ray | 1.55 Å | A/C=3-492 |
| 5BVG | X-ray | 1.6 Å | A/C=1-492 |
| 6OP3 | X-ray | 1.6 Å | A/C=4-480 |
| 7MCI | X-ray | 1.65 Å | A/C=1-492 |
| 6BBL | X-ray | 1.68 Å | A/C=1-492 |
| 6O7P | X-ray | 1.7 Å | A/C=1-492 |
| 6OP1 | X-ray | 1.7 Å | A/C=4-480 |
| 6VXT | X-ray | 1.74 Å | A/C=1-492 |
| 5CX1 | X-ray | 1.75 Å | A/C/E/G/I/K/M/O=1-480 |
| 6O7N | X-ray | 1.75 Å | A/C=1-492 |
| 6UG0 | X-ray | 1.83 Å | A/C=1-492 |
| 6O7O | X-ray | 1.89 Å | A/C=1-492 |
| 4WZA | X-ray | 1.9 Å | A/C=4-480 |
Showing 20 of 88 experimental structures (best resolution first).
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