Comparing the matches with your query

The ‘view superposed’ button (shown by arrow in Figure 5) launches a molecular viewer window showing the superimposed domains, similar to that in Figure 6. This is an interactive viewer so you can rotate the superimposition to get a good view of the toxin functional subdomains.

Please note, the Jmol viewer runs a version of Java that is not supported by most modern browsers. To overcome this you could ‘download’ both the ‘Query PDB’ and ‘Target PDB’, by right clicking and saving them as ‘.pdb’ files. Then view the superposed structures in a separate visualisation software like Mol* (https://molstar.org/viewer/).

In the view here we have also used coloured brackets alongside to show the positions of the stem (red), rim (yellow), and β-sandwich (blue) subdomains. By rotating the superimposition in your own session, you should see that the elements of the query 1pvl are in darker colours whilst those of the matched 1tr5 structure are in lighter colours. Elements that could not be matched in the superimposition are shown in dark and light grey (for the query and the hit, respectively). Loops connecting matched SSEs are also coloured provided that their backbone atoms superimpose well.

Most of the time you can inspect the superimposition and recognise β-strands or α-helices that are most likely equivalent but have not been matched by PDBeFold because they have altered position too much between the two structures. The program has left them out to improve its Q-score for the match, but sometimes looking by eye you will realise that the local structural differences are biologically significant.