Primary structure refers to the amino acid sequence, or multiple sequences of a protein. Each amino acid in a primary structure is known as a residue. Because the 20 amino acids have individual chemical and physical properties, they influence the 3D structure, the function of the protein and its chemical properties. i.e. hydrophobic and hydrophilic properties.

Ions can additionally be found in the primary structure. Zinc and calcium ions can form complexes that are present in the protein's primary structure.