Chemical synthesis of proteins has enabled the synthesis of hundreds of proteins, not all proteins are accessible through typical ligation conditions. One particularly challenging protein is a 125-residue human phosphohistidine phosphatase 1 (PHPT1), whose three cysteines near the protein’s C-terminus are not strategically placed for ligation. Here, PHPT1 was prepared from three unprotected peptide segments using two ligation reactions at cysteine and alanine junctions. Selenazolidine was utilized as a masked precursor for N-terminal selenocysteine in the middle segment, and, following ligations, deselenization provided the native alanine residue. This approach was used to synthesize both the wild-type PHPT1 and an analog in which the active-site histidine was substituted with the unnatural and isosteric amino acid β-thienyl-L-alanine. The activity of both proteins was studied and compared, providing insights into the enzyme’s active site.