Detailed view of Aβ 1–7 bound to 3D6. A) 3.0 sigma electron density omit map (calculated while omitting the Aβ peptide from the model for phase calculations) is shown in orange. Protein and peptide are shown in stick representation with oxygens colored red, nitrogens in blue, carbons in orange for the peptides, light blue for the light chain and cyan for the heavy chain. B, C, D, E) The surface of the heavy chain is shown in cyan and light chain in light blue. Aβ peptide is shown in stick representation with oxygens colored red, nitrogens in blue and carbons in orange. In B only, peptide Asp-1 is shown. Asp-1 is buried inside a deep cave on the surface of the antibody. In C, D and E a mesh, representing the surface of the peptide, is shown to illustrate the actual volume of the peptide in the cave, note: the side chain of residue 6 is not visible beyond the Cβ atom of His-6. C) top view. D) side view. E) side view slice illustrating the depth of the cave.