- Course overview
- Search within this course
- What is PDBeFold?
- PDBeFold for structural comparison in the Leukotoxin family
- Starting up PDBeFold from the PDBe homepage
- Search results for PDB entry 1pvl
- Comparing the matches with your query
- Summary
- Your feedback
- Learn more
- Get help and support on PDBeFold
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Getting more from your results
To look in detail at any returned structural match just click on the underlined number in the first column (arrowed in Figure 4).
The summary for the top 1t5r hit in our search (match 9) is shown in Figure 5. You can see that our Panton Valentine Leukotoxin F component 1pvl query is on the left and the S component 1t5r match is on the right. In the middle are the details of the superimposition from the structural alignment that PDBeFold has done. A total of 17 SSEs were matched satisfactorily between the two structures corresponding to 245 residues (Nalgn) and with an RMSD of 1.419Å.
Below the table is a quick summary of the secondary structure alignment – ‘S’ represents aligned strands and ‘H’ represent aligned helices (‘s’ and ‘h’ are for elements that don’t align well or which correspond to a loop in one of the structures). The superimposed coordinates can also be downloaded from this page.
At the bottom of the results page is a detailed matching of residue ranges. Although complicated, this can be very helpful if, for example, you want to write out a residue selection to make an image with equivalent colouring between matched parts of two structures.
Finally, below the residue ranges summary is a detailed table of matches between the query and the hit on a residue-by-residue basis. This can be helpful in preparing a structure-based alignment of the protein sequences. Or it may highlight significant differences where a residue in the equivalent three-dimensional position in a domain has changed its character markedly – perhaps to adapt the fold to a new function.
Click on the ‘view superposed’ button (mouse arrow in Figure 5).
Please note, the Jmol viewer runs a version of Java that is not supported by most modern browsers. We are working to replace this viewer, however in the meantime you may change the ‘Viewer’ option to Rasmol – clicking ‘view superposed’ will then download a PDB-formatted file named ‘send.rasmol’ which can be opened in a separate visualisation software.