Figure 5: Pockets visualization and substrate docking. | Nature Communications

Figure 5: Pockets visualization and substrate docking.

From: X-ray structure of a CDP-alcohol phosphatidyltransferase membrane enzyme and insights into its catalytic mechanism

Figure 5

(a) Putative ligand-binding pockets of DIPPS assigned with HOLLOW21 (top view from the cytoplasm-facing side). The pockets are shown in pink (1), orange (2) and blue (3). (b) Detailed view of conserved pocket 1. The strictly conserved residues Gly361, Ala364 and Gly374, belonging to the family consensus sequence, form the surface of the pocket. (c) Model with bound ligands in DIPPS domain. The ligands fit well into the surface cavities and are properly oriented. (d) Position of DIPPS substrates relative to the bilayer surface. The CDP moiety is above the bilayer surface, whereas the inositol group of CDP-inositol and inositol-phosphate are slightly underneath it. The membrane position was estimated using the PPM server49.

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