Figure 4. Tunnels and cavities in CPS1.

Overall views (center) of tunnels and cavities (surface representation) in (a) the ligand-bound and (b) the apo forms of CPS1. The carbamate tunnel linking the two phosphorylation active sites (see text) is well defined only in the ligand-bound conformation. Boxes at both sides show detailed views of the structural elements forming the carbamate tunnel. The tunnel loop (colored green) and the T′-loop (colored orange) occlude in the ligand-bound form many of the cavities found in the apo form. Some side chains are explicitly shown to highlight the structural changes. A possible ammonia tunnel, which remains invariant between the apo and ligand bound forms, is depicted in the central box. Residues at the entrance to this tunnel and at the conserved gate are shown with carbon atoms colored yellow and cyan, respectively.