Photosystem II D2 protein (psbD) is a 342-residue protein from Thermostichus vulcanus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: D0VWR8.
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The mean pLDDT of this model is 98.3 (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 | 99% |
| 70 to 90 | Confident: backbone generally right | 1% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
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 (PubMed:19433803, PubMed:23426624). 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
Cellular thylakoid membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5B66 | X-ray | 1.85 Å | D/d=1-342 |
| 5B5E | X-ray | 1.87 Å | D/d=1-342 |
| 3WU2 | X-ray | 1.9 Å | D/d=1-342 |
| 5V2C | X-ray | 1.9 Å | D/d=1-342 |
| 4UB6 | X-ray | 1.95 Å | D/d=1-342 |
| 4UB8 | X-ray | 1.95 Å | D/d=1-342 |
| 7D1T | EM | 1.95 Å | D/d=1-342 |
| 8GN2 | X-ray | 1.95 Å | D/d=1-342 |
| 7D1U | EM | 2.08 Å | D/d=1-342 |
| 4IL6 | X-ray | 2.1 Å | D/d=1-342 |
| 8GN1 | X-ray | 2.1 Å | D/d=1-342 |
| 6JLJ | X-ray | 2.15 Å | D/d=1-342 |
| 6JLK | X-ray | 2.15 Å | D/d=1-342 |
| 6JLL | X-ray | 2.15 Å | D/d=1-342 |
| 8GN0 | X-ray | 2.15 Å | D/d=1-342 |
| 8IR5 | X-ray | 2.15 Å | D/d=1-342 |
| 8IR6 | X-ray | 2.2 Å | D/d=1-342 |
| 8IR9 | X-ray | 2.2 Å | D/d=1-342 |
| 8IRA | X-ray | 2.2 Å | D/d=1-342 |
| 7COU | X-ray | 2.25 Å | D/d=1-342 |
Showing 20 of 47 experimental structures (best resolution first).
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