Ligand: Difference between revisions
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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. | 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 ions. 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|standard residues]]. | 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 ions. 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|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|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] ''non-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|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] ''non-standard residues''. | ||