Ligand: Difference between revisions
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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. | 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 | 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|standard residues]]. | ||
Depending on the way in which the PDB file is structured, ''ligand'' can include either an entire phosphotyrosine residue, or only the covalently linked phosphate. | Depending on the way in which the PDB file is structured, ''ligand'' can include either an '''entire phosphotyrosine residue''' [[because that is a [[Non-Standard Residue|non-standard residue]], or '''only the covalently linked phosphate'''. | ||
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. | 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. | ||