Tertiary structure of a Protein Even when the polypeptide chain takes its secondary structure, it's not yet a fully folded, functional protein. To become functional, the polypeptide chain has to take on a specific three-dimensional shape, which is determined by the interactions of the amino acid side chains. This shape is called the tertiary structure of the protein. For example, myoglobin, which is shown in the following figure, is a type of protein that exists in the muscles of animals. This protein is formed from eight -helices surrounding an iron-containing heme, which binds oxygen. heme c G F h e B D