Fig. 2.

Superposition of the 4 independent Fabs in PDB structure 5K8A. For each folding unit of each polypeptide, its 4 independent structures are superposed. Backbone ribbons for L and H chains are shown using the rainbow color convention from blue to red, with the endpoints of each labeled. Sidechains with non-uniform rotamers are emphasized by thick bonds in varied colors; about 20% of the sidechains in each domain exhibit this rotamer variation, usually in surface loops that are involved in crystal contacts (contacts not shown). Residues with conserved rotamers are shown using thin bonds. Dashed lines show the breakpoints (at Fab elbows) used for the domainwise alignment. Note that the CDR loops are at the top in both chains. (A) Superpositions of the two folding units of the light chains (i.e., chains L, M, A and E). (B) Superpositions of the two folding units of the heavy chain (chains H, V, B, and F). The pyroglutamate residue (pGlu) at the N-terminus of the heavy chain is labeled.