Pursuing artificial mimics of natural protein structures is a critical research area with broad implications in biochemistry, synthesis, and materials science. A key objective is to understand and validate the chirality transfer process from small molecules, such as amino acids, to complex three-dimensional (3D) architectures. Despite significant progress, only a limited number of artificial materials with well-defined, protein-like crystalline structures have been reported due to the inherent challenge of balancing structural rigidity and flexibility. Typically, rigidity enhances structural integrity and facilitates characterization, whereas flexibility enables greater functional versatility. In this study, by using a cysteine-derived linker that integrates both rigid and flexible motifs, we report the synthesis of homochiral metal-organic frameworks L/D-Zn-PDT-α and L/D-Zn-PDT-β, featuring helical and pleated-sheet structures, respectively. An in situ crystal transformation from Zn-PDT-α to Zn-PDT-β is closely monitored, disclosing a transition pathway from a relatively rigid to a more flexible crystalline phase. Systematic crystallographic analyses demonstrate how the coordination mode (bidentate versus monodentate) dictates the rigidity or flexibility of the resulting 3D structure. Owing to their structural adaptability, L/D-Zn-PDT-β frameworks serve as homochiral hosts capable of accommodating achiral organic dyes, thereby inducing notable chiroptical activities. The insights obtained from the structural study may have broader implications for the design of other chiral assemblies beyond this work.