Clustering of V, D, and J region structures. These panels show representative clusters of structures with the same V (Panel A), D (Panel B), and J (Panel C) regions, respectively. All structures in the same cluster have the same color. For the VH V region and VL, the clustering worked well. However, for the VH D and J regions the clustering procedure did not work (i.e., antibodies with the same germline regions have different structures). Interestingly, all of the deviations occur within CDR3. This observation led to the development of an alternative delimitation of structure: V* (everything before CDR3, FR1-FR3, IMGT positions 1-104), CDR3, and J* (everything after CDR3, FR4, IMGT positions 118-128).