Ligand

From Proteopedia

In its usual sense, ligands denotes small molecules bound non-covalently to macromolecules. The binding is reversible. Examples: Receptors bind hormone and cytokine ligands, and enzymes bind substrate or inhibitor ligands. Avidin binds the ligand biotin. See also Ligands (Biochemistry) in Wikipedia.

In macromolecular structure, ligand has a specialized meaning derived from the way in which the PDB file format is structured. All atoms in PDB files are classified into two groups: atoms in protein or nucleic acid chains, identified with the ATOM record type, and all other atoms, which are identified with the HETERO record type.

Many visualization and modeling programs further divide hetero atoms into solvent and non-solvent atoms. Solvent includes water and common anions such as sulfate and phosphate. These programs (e.g. RasMol, Chime, and Jmol) often define ligand to include all non-solvent