Streptococcus pyogenes is a common pathogenic Gram-positive bacterium causing worldwide diseases with high morbidity and mortality every year. Metalloproteins have been highlighted for their essential roles in the metabolisms and virulence of pathogens. In this study, Cu-binding proteins of Streptococcus pyogenes were isolated by using immobilized metal ion chromatography and identified with LC-MS/MS. Totally, 21 proteins were identified and the network of interactions of the proteins was established. These proteins function in many biological processes such as translation, metabolism and ion transporting.