The hydrophobic pocket and the variable loop conformation. (A) The hydrophobic pocket in the DC-LAMP domain was filled with water molecules, which are displayed as a red surface, using HOLLOW . (B) Structural alignment of DC-LAMP chain A (grey) and B (blue). Hydrogen bonds connect loop L1 to an adjacent hairpin in chain A, but not in chain B. (C) A VH immunoglobulin domain is shown for comparison (PDB 1IGT). Complementarity determining regions (CDR) are drawn as red loops. The two β-sheets of the domain, displayed in green and blue, are connected by a disulfide bond (S-S).