STRUCTURAL CLASSIFICATION

Structure classification can be done by using the following databases:

  1. SCOPe
  2. CATH

SCOPe

We can do our Structural classification of our model protein using the SCOPe database. First i did a 3D-Blast of our Model Protein i.e K8G1J4 and that resulted in a SCOPe ID. Using this SCOPe ID we can check the protein's Class,Fold,Superfamily,Family,Protein name,Species to which the model protein belongs to. We get an output as follows:

SCOP_RESULTS

Figure shows the Class,Fold,SuperFamily,Family,Protein and Species names


CATH

CATH shares many broad features with the SCOP resource, however there are also many areas in which the detailed classification differs greatly.
The four main levels of the CATH hierarchy are: Class,Architecture,Topology,Homologus Super family. We search the CATH database using sequence search and obtained a set of 34 matches. The best match was with the 1t1g.a protein. This can be seen as follows:

CATH_DOMAIN

The following were the CATH results:

CATH_DOMAIN

We can also view in this pdf how the Super Family is classified for Domain 3.40.50. Domains have been grouped into S35, S60, S95, S100 clusters which reflect increasingly strict sequence identity cutoffs. For example, all domains grouped into the same S35 cluster are guaranteed to share at least 35% sequence identity.
To view the Super Family superposition click here