Hetero atoms: Difference between revisions
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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== | ==See Also== | ||
[[Atomic coordinate file]] | *[[Atomic coordinate file]] | ||
[[Protein Data Bank]] | *[[Protein Data Bank]] | ||
[[Standard | *[[Standard Residues]] | ||
[[Non- | *[[Non-Standard Residues]] | ||
*[[Ligand]] | |||
Latest revision as of 22:18, 14 January 2020
In the 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.
Standard Residue LigandsStandard 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.
DipeptidesDipeptides
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 ResidueFinding Models Containing a Residue
At RCSB.Org, using the Advanced Search and query type Chemical ID, you can find all entries in the database that contain a particular chemical component. For example, in December, 2019, five entries contain PYL (explained in Non-Standard Residues).
A complete list of all compounds in the PDB is available, including hydrogens, 3D structures, and bond orders, in the Chemical Components Dictionary of the Worldwide Protein Data Bank. This includes all Standard Residues as well as Non-Standard Residues, carbohydrate adducts, Ligands and Hetero Groups. It is updated weekly for newly released entries.