Lead is a toxic metal harmful to human beings because of its long history and wide use in human society. The interaction of lead with proteins is one of the most common ways it exerts toxicity. Due to its thiophilic property, lead targets thiol-rich proteins with high affinity and forms stable Pb-S bonds, which may replace the originally bound metal ion and incapacitate the protein/enzyme. Thus, the knowledge of the Pb-S bonds in proteins is important. To study Pb-S bonds, we chose a de novo designed protein α3DIV, able to bind Pb(II) via its three cysteines, as the model protein. Using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS), we proved the formation of a triangular pyramidal PbS3 site in α3DIV by detecting specific Pb-S bond rupture signals, including the previously undetected Pb-S(Cys67) bond. Moreover, the pH-dependent weakening of Pb-S bond strength was revealed and quantified, leading to the dissociation of the PbS3 site at pH 4.5.