Hetero atoms: Difference between revisions

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Eric Martz

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-In the [[PDB files|PDB data file format]] for macromolecular models, each atom is designated either ATOM or HETATM (which stands for ''hetero atom''). ATOM is reserved for atoms in [[standard residues]] of protein, DNA or RNA. HETATM is applied to [[non-standard residues]] of protein, DNA or RNA, as well as atoms in other kinds of groups, such as carbohydrates, substrates, [[ligands]], solvent, and metal ions.
+In the [[PDB files|PDB data file format]] for macromolecular models, each atom is designated either ATOM or HETATM (which stands for '''hetero atom'''). ATOM is reserved for atoms in [[Standard Residues|standard residues]] of protein, DNA or RNA. HETATM is applied to [[Non-Standard Residues|non-standard residues]] of protein, DNA or RNA, as well as atoms in other kinds of groups, such as carbohydrates, substrates, [[ligands]], solvent, and metal ions.
+===Standard Residue Ligands===
+Standard amino acids, nucleosides, nucleotides (or nucleobases) are designated HETATM when they are "ligand", that is, when they are isolated, free single monomeric residues, not part of a polypeptide/protein or polynucleotide chain. Examples are glycine in [[6rs6]], tryptophan in [[6hip]], and cytidine-5'-monophosphate "C" in [[1kdo]].
+====Dipeptides====
+Standard amino acids in '''dipeptide''' ligands are also designated HETATM by convention of the [[PDB]]. An example is Ala-Pro in [[2cyh]]. Dipeptide ligands are given the same chain ID as the chain to which they are bound. In contrast, '''tripeptides and longer polypeptides''' are designated ATOM and given unique chain IDs. An example is Tyr-Pro-Tyr in [[1hqw]].
+===Finding Models Containing a Residue===
+{{Template:Chemical Components}}
 ==See Also==
-[[Atomic coordinate file]]
+*[[Atomic coordinate file]]
-[[Protein Data Bank]]
+*[[Protein Data Bank]]
-[[Standard residues]]
+*[[Standard Residues]]
-[[Non-standard residues]]
+*[[Non-Standard Residues]]
+*[[Ligand]]