Equivalence classes organized by Integrated Functional Elements (IFEs)
In the past, we created equivalence classes of PDB files according to the longest chain in the structure. For example, we looked at the ribosomal large subunit but ignored the 5S rRNA and any tRNAs. Now that we work with mmCIF files, we have started making equivalence classes at a more detailed level. For example, a eukaryotic ribosomal RNA may have a large and small subunit, 5S rRNA, 5.8S rRNA, tRNAs, and mRNA. The LSU and 5.8S rRNA are considered to be an Integrated Functional Element because they make large numbers of Watson-Crick between the two chains, and so are considered together when forming equivalence classes. However, the small subunit, 5S rRNA, and tRNAs stand as separate molecules, and so separate equivalence classes are made for them. For example, visit the representative set at this page and filter by the text 3J7R to see the equivalence classes with IFEs from the Sus scrofa 3D structure, which contains the LSU integrated functional element involving chains 5 and 8 and denoted by 3J7R|1|5+3J7R|1|8, the SSU involving chain S2 and denoted by 3J7R|1|S2, the 5S rRNA in chain 7 and denoted by 3J7R|1|7, and the tRNAs in chains S5 and S6.