The protein tertiary structure is the overall spatial arrangement of one polypeptide chain. It includes how its protein secondary structures and intervening regions fit together. For example, the schematic under protein places positions 4 and 9 near each other despite their separation in protein primary structure. Such cooperation can help construct an active site; sequence distance and spatial separation answer different questions. Hydrophobicity, backbone hydrogen bonds and other interactions help stabilize folds, and some proteins additionally contain protein disulfide bonds. See Cooper: tertiary structure and interactions between chain regions.
A protein binding site is a region of a protein structure that interacts with a ligand. Its arrangement of amino acid residues helps determine recognition; connecting loops supported by a beta sheet can contribute to it. An enzyme's active site binds a substrate and accelerates a chemical reaction. See Alberts et al.: protein binding sites and active sites.
A protein disulfide bond is a disulfide bond linking two sulfur chemical atoms carried by suitable amino acid residues. It can connect distant portions of a polypeptide chain or different chains. See Cooper: sulfur-containing residues and disulfide crosslinks. The four internal protein disulfide bonds of ribonuclease A are central to the ribonuclease A refolding experiment; breaking these crosslinks need not break the peptide bonds along its protein backbone.
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