Table 1.
Comparison of Pc–Cyt f complex structures shown in Figure 4. The names of columns and rows correspond to the panels in Figure 4. (a) Central structure of encounter complexes cluster obtained by BD for spinach Pc and turnip Cyt f. (b) Final complex obtained by all-atom MD, initiated from the structure in panel (a). (c) Complex of spinach Pc and turnip Cyt f predicted by AlphaFold 3 with the highest ipTM score. (d) Complex of spinach Pc and turnip Cyt f predicted by AlphaFold 3 with the lowest ipTM and the highest EDC scores. (e) Complex of spinach Pc and spinach Cyt f predicted by AlphaFold 3 with the lowest ipTM and the highest EDC scores. (f) Complex of spinach Pc and spinach Cyt bf predicted by AlphaFold 3 with the highest ipTM and the highest EDC scores. (g) NMR structure (PDB id 2pcf, model 9) for spinach Pc and turnip Cyt f. (h) NMR structure (PDB id 1tkw, model 7) for poplar Pc and turnip Cyt f. Outlined diagonal values stand for Cu–Fe distance|EDC score; upper triangle values on a grey background stand for distances between Pc centers of mass in two structures; lower triangle values stand for RMS distances between Pc Cα atoms in two structures. All distances are presented in Angstroms.
| Structure | a | b | c | d | e | f | g | h |
|---|---|---|---|---|---|---|---|---|
| a | 28.4|0.026 | 17.5 | 15.5 | 15.9 | 15.9 | 14.4 | 15.3 | 19.3 |
| b | 21.2 | 14.3|0.056 | 2.7 | 2.2 | 2.0 | 3.2 | 7.0 | 7.9 |
| c | 20.5 | 4.2 | 13.3|0.055 | 1.9 | 1.3 | 1.9 | 7.2 | 9.5 |
| d | 20.7 | 3.3 | 2.4 | 12.6|0.059 | 0.7 | 1.6 | 5.5 | 7.6 |
| e | 20.6 | 3.1 | 2.0 | 0.9 | 12.8|0.058 | 1.5 | 6.2 | 8.3 |
| f | 19.0 | 3.9 | 2.4 | 2.3 | 2.4 | 13.9|0.059 | 5.7 | 8.3 |
| g | 19.4 | 7.7 | 9.2 | 7.1 | 7.7 | 7.4 | 11.4|0.052 | 4.5 |
| h | 23.1 | 9.5 | 11.4 | 9.7 | 10.3 | 9.9 | 6.6 | 14.2|0.046 |