Displaying the results

This is a general rule for PDBeFold searches – the most interesting hits are often at the bottom of the table on the very last page of the results!

The interface provides you with a ‘last page’ button to go there quickly. Another good tip is to change the ‘Sort by’ pull-down (at the bottom of the table) to ‘Seq %’ instead of ‘Q score’. The last entries on the last page will then have hits with little sequence identity to your query but high structural similarity – these may be homologues that you may have not found with a simple sequence search. 

Although it may seem a bit odd to see our query returned from the search, PDBeFold is searching the whole PDB archive for us – so as long as 1pvl is in the archive, it should be found and be a perfect hit!

In fact several other hits appear in the top half of the table that are related structures of the Panton Valentine Leukotoxin F component. This often happens as the PDB will typically contain multiple entries of the same protein from different experiments, crystal forms, or with different small molecules bound. From its title you might guess that 2qk7 also has the S component in it; however, interestingly PDBeFold has in fact only matched the F component (which is chain B in this entry)!