Figure 6

Examples of superimposition of proteins displaying rotational symmetry. a) Standard superimposition of the C-reactive protein (CRP) PDB IDs: 1gnh (green) and 1b09 (lilac). The quaternary structure consists of five identical chains (homo-oligomer) and is classified as a cyclic group C5. The optimal permutation of chains was: R: a,b,c,d,e; T: d,e,a,b,c and led to a standard RMSD of 1.01 Å (for the 1030 Cα atoms), b) Weighted superimposition of the protein RepB, PDB IDs 3dkx (green) and 3dky (lilac). The quaternary structure consists of 6 identical chains (homo-oligomer), being classified as cyclic groups C2 and C3, respectively. Because of the high flexibility of the protein, the weighted RMSD provided a better overall superimposition, and led to a weighted Cα RMSD of 0.92 Å (536/1159 atoms), c) Standard superimposition of the Glutamine Synthethase Class I (GSI) from Salmonella typhymurium, PDB IDs 1fpy (green) and 1f1h (lilac). The quaternary structure consists of 12 identical chains (homo-oligomer) arranged as a ring and classified as dihedral group D6. In this case, the optimal permutation of chains was that in the PDB files, that led to a standard RMSD value of 0.71 Å (5304/5616 Cα atoms), d) Standard superimposition of human deoxyhemoglobin, PDB IDs 1fdh (green) and 2hhb (lilac). The quaternary structure is a tetrameric hetero-oligomer (α₂β₂) and is classified as a cyclic group C2. The results revealed that the optimal permutation of chains was: R: a,g,b,h; T: a,b,c,d that led to an standard RMSD value of 0.42 Å (574 Cα atoms).