Ligand

In its usual sense, ligand denotes a small molecule bound non-covalently to a macromolecule. The binding is typically 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 and somewhat different 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 hetero atoms. In these programs, selecting and displaying ligand will display, for example, all carbohydrate, whether or not covalently linked to a protein, in addition to moieties ordinarily considered to be ligand, such as metal ions and small organic compounds other than standard residues.

Depending on the way in which the PDB file is structured, ligand can include either an entire phosphoserine residue because that is a non-standard residue, or only the covalently linked phosphate. For example, in 1apm the phosphite ions ligands [PO3] are covalently linked to phosphoserine and phosphothreonine, whereas in 1bkx the same entities are deemed [SEP] and [TPO] ligands.

On the other hand, some things that would ordinarily be considered to be ligands will fail to be included when ligand is selected and displayed in Jmol (or RasMol or Chime). These include single amino acids or nucleotides, peptide ligands, DNA or RNA bound to a protein as ligands.