Ligand: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Jaime Prilusky, Eran Hodis, Eric Martz, Wayne Decatur

@@ Line 3: / Line 3: @@
 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.
+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 [[Standard Residues|standard residues]] of protein or nucleic acid chains, identified with the ATOM record type, and all other atoms, which are identified with the [[HETATM]] 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''.
+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. [[FirstGlance in Jmol]] uses special code to display single [[Standard Residues|standard residues]] or [[Non-Standard Residues|non-standard residues]] as ligand, which avoid them being invisible in a backbone-only display such as a secondary structure schematic cartoon.
-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.
+{{Template:Chemical Components}}
+The [http://www.pdbbind.org.cn/| PDBbind Database] provides a comprehensive collection of annotations of experimentally measured binding affinities, such as Kd, Ki, or IC50, for all biomolecular-ligand complexes deposited in the Protein Data Bank (PDB).
 ==More About "Ligand"==
@@ Line 18: / Line 20: @@
 *Ligand in the [http://www.rasmol.org/software/RasMol_2.7.4.2_Manual.html#predefinedsets RasMol 2.7 Reference Manual]
 *[http://www.umass.edu/microbio/rasmol/seleccmd.htm Select Commands in Chime and RasMol]
+===See Also===
+* [[Atomic coordinate file]]
+* [[PDB file format]]