The amino acid sequence, or so-called primary structure, of a protein actuates the folding and intramolecular bonding of the linear amino acid chain, which determines the protein's unique three-dimensional structure. Hydrogen bonding between amino groups and carboxyl groups in neighboring regions of the actual amino acid residues chain can result in highly regular local secondary structures such as alpha helices and beta sheets.

Most proteins comprise several alpha helices and beta sheets which are the most common structural elements. However, other less common patterns such as beta turns and omega loops occur as well. When multiple polypeptide chains interact and form a protein macromolecule, then this is called a quaternary structure.

Protein structures can be determined using nuclear magnetic resonance spectroscopy (NMR) or X-ray crystallography. For larger protein complexes, cryo-electron microscopy can be used to determine protein structures. The structure of a protein can give more insights into the function of that protein.