We report the crystal structure of human PITPα in complex with microcolin H at 2.0 Å resolution, revealing that microcolins bind covalently within the lipid-binding cavity and stabilize PITPα in an open conformation with a markedly enlarged cavity relative to the lipid-bound state. These results define the structural basis of PITP inhibition by microcolins and underscore the importance of using ligand-bound conformations for accurate structure-based modeling.