Photosystem II D2 protein (psbD1) is a 352-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: Q8CM25.
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The mean pLDDT of this model is 96.9 (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 | 1% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors. D2 is needed for assembly of a stable PSII complex
PSII is composed of 1 copy each of membrane proteins PsbA, PsbB, PsbC, PsbD, PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX, PsbY, PsbZ, Psb30/Ycf12, peripheral proteins PsbO, CyanoQ (PsbQ), PsbU, PsbV and a large number of cofactors. It forms dimeric complexes. Part of a photosystem II (PSII) assembly intermediate complex PSII-I; crystallized from a strain deleted of psbJ, it forms…
Cellular thylakoid membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9EVX | EM | 1.71 Å | D/d=1-352 |
| 7RF1 | X-ray | 1.89 Å | D/d=1-352 |
| 7YQ2 | X-ray | 1.9 Å | D/d=1-352 |
| 7YQ7 | X-ray | 1.9 Å | D/d=1-352 |
| 8F4C | X-ray | 2.0 Å | D/d=1-352 |
| 8F4I | X-ray | 2.0 Å | D/d=1-352 |
| 8F4J | X-ray | 2.0 Å | D/d=1-352 |
| 6W1T | X-ray | 2.01 Å | D/d=1-352 |
| 7RF6 | X-ray | 2.01 Å | D/d=1-352 |
| 8F4F | X-ray | 2.03 Å | D/d=1-352 |
| 8F4G | X-ray | 2.03 Å | D/d=1-352 |
| 6DHP | X-ray | 2.04 Å | D/d=12-352 |
| 6DHE | X-ray | 2.05 Å | D/d=12-352 |
| 6DHO | X-ray | 2.07 Å | D/d=12-352 |
| 6DHF | X-ray | 2.08 Å | D/d=12-352 |
| 6W1O | X-ray | 2.08 Å | D/d=1-352 |
| 7RF2 | X-ray | 2.08 Å | D/d=1-352 |
| 11YO | X-ray | 2.09 Å | D/d=1-352 |
| 6W1U | X-ray | 2.09 Å | D/d=1-352 |
| 6W1V | X-ray | 2.09 Å | D/d=1-352 |
Showing 20 of 65 experimental structures (best resolution first).
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