The binding mechanism between the engineered C domain of the Amsphereâ„¢ A3 protein A (PrA) ligand and a VHH single domain antibody (sdAb) was revealed. Binding sites in the PrA ligand in helices 2 and 3 and in framework regions 1 and 3 of the VHH were confirmed. Identified VHH residues are not involved in antigen recognition. Overlap with a human VH showed the same interaction sites. These results provide insight on why Amsphere A3 is a suitable tool for…