Ligand: Difference between revisions
Eric Martz (talk | contribs) →More About "Ligand": adding content |
Eric Martz (talk | contribs) Added links to software |
||
| Line 5: | Line 5: | ||
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''. | ||
Revision as of 07:06, 23 May 2009
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.
The green links that Proteopedia places beneath molecules under the category Ligands are based on a somewhat different definition, as explained below.
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.
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] non-standard residues.
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.
More About "Ligand"More About "Ligand"
- See Atom Expressions in the Jmol Reference Manual. If that link is broken, try Documentation at Jmol.Org.
- Ligands (Biochemistry) in Wikipedia.
- Ligand in the RasMol 2.6 Reference Manual
- Ligand in the RasMol 2.7 Reference Manual
- Select Commands in Chime and RasMol