Photosystem I reaction center subunit II (psaD) is a 139-residue protein from Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P0A420.
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The mean pLDDT of this model is 95.5 (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 | 2% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7FIX | EM | 1.97 Å | D1/D2/D3=1-139 |
| 1JB0 | X-ray | 2.5 Å | D=2-139 |
| 7M75 | X-ray | 2.75 Å | D=2-139 |
| 6TRA | EM | 2.85 Å | D=1-139 |
| 6PFY | X-ray | 2.9 Å | D/O/b=1-139 |
| 6PGK | X-ray | 2.9 Å | D/O/b=1-139 |
| 6TRC | EM | 2.98 Å | 4/D/d=1-139 |
| 7M76 | X-ray | 3.0 Å | D=2-139 |
| 7M78 | X-ray | 3.0 Å | D=2-139 |
| 6TRD | EM | 3.16 Å | 4/D/d=1-139 |
| 6LU1 | EM | 3.2 Å | D=1-139 |
| 9LZJ | EM | 3.4 Å | aD/bD/cD=1-139 |
| 9LZK | EM | 3.5 Å | D=1-139 |
| 1C51 | X-ray | 4.0 Å | - |
| 2PPS | X-ray | 4.0 Å | - |
| 5ZF0 | X-ray | 4.2 Å | D1/D2/D3/D4/D5/D6=2-139 |
| 4FE1 | X-ray | 4.92 Å | D=2-139 |
| 7BW2 | X-ray | 6.5 Å | D=1-139 |
| 3PCQ | X-ray | 8.98 Å | D=2-139 |
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