Search by structure in CATH

The search by structure uses the CATHEDRAL server which runs a structural comparison algorithm to compare a protein of interest (otherwise known as the ‘query structure’) against domains already classified in the CATH database (Figure 11). This means you can try to identify an unknown protein by comparing it with all known structures in CATH.

Let’s do it together: identify the CATH superfamily for a query structure ‘4i6g‘

The PDB structure, 4i6g, is an X-ray crystallography-solved structure for which the function has yet to be determined. However, this can be inferred by comparing it with other proteins of known function by following steps:

1. Open the CATHEDRAL server.
2. Download the structure coordinate file (.pdb format) for 4i6g from the PDB website.
3. Upload the downloaded 4igg.pdb file in the CATHEDRAL server (using ‘Choose File’ option) and select ‘Submit’.
4. The server loads the name and the constituent chains of the uploaded PDB and displays it in a new page (Figure 12).

5. As suggested in the result page (blue box in Figure 12), each of the identified PDB chains can be submitted for structural scans separately. Submit chain A of the uploaded PDB to the structural scan by clicking on ‘Submit Structure’ for chain A.

6. If the servers are busy, you might find that the job takes quite a long time to complete – you can skip the wait and view the previously calculated results for our query structure below (Figure 13). Explore the results by clicking on the  below.

Figure 13 Calculated results after submitting Chain A of 4i6g.