Alignment of the Dynamin A GTPase domain and the cpGTPase domain from the YjeQ. Topologies of (a) the Dynamin A GTPase (SCOP domain d1jwyb_) and (b) cpGTPase domain from the YjeQ protein (d1u0la2). Aligned SSEs are indicated by lighter colors. (c) DEDAL superposition of the GTPase and the cpGTPase domains (yellow and blue, respectively). For clarity, only the aligned parts of the structures are shown. (d) View of the binding site in the same superposition showing residues participating in the GDP/GTP binding (red) and the GDP molecule. Despite significant topological differences, DEDAL effectively handles all alignable SSEs and correctly superimposes the active sites. The sequence identity of the superimposed regions is 24.2%.