The similarity between the human monoamine oxidase B (2v61, left) and an electron transfer flavoprotein from Methylophilus methylotrophus (3clt, right). These proteins belong to two different folds of the “Rossmann-like” group and probably share a remote ancestor [Aravind L et al., Curr Opin Struct Biol. (2002), 12:392–399].

Even though these folds are related the fold comparison program DaliLite finds an alignment with a non-significant score that fails to correctly superpose the ligands. Conversely superpose3D finds a structural match comprising eight residues with an RMSD of 0.64 Å (the residues comprising the beta-sheets were not used in the comparison). The program correctly identifies the similarity between the two binding sites. Interestingly in this case using a representation that includes side-chain information resulted in a different yet still meaningful match.