Ligands and metalsAny unique ligands and metals in the structure have their own page. An example is given below.
a-c. Thumbnail image, list of ligands and list of metalsThe left-hand side of the ligands/metals page is similar to the top page and is as shown below.
d. Ligand molecule
The ligand molecule is shown both as a 3D image, and as a 2D chemical plot. Clicking on the RasMol icon in the middle will display the ligand molecule in RasMol.
The icon below the RasMol icon gives a flattened picture of the ligand molecule in PostScript, with all the atoms labelled with their atom names.
The chemical diagram of the ligand molecule on the right has been automatically flattened from the 3D structure using the LIGPLOT program, so may look odd for really difficult molecules (eg ones with multiple rings). It shows any double or triple bonds - as annotated in the PDB's Het Group Dictionary.
The LIGPLOT diagram displays a schematic diagram of all the interactions (in terms of hydrogen bonds and non-bonded contacts) made between the ligand, or metal, and the residues of any protein molecules in the structure.
Hydrogen bonds are shown as green dotted lines labelled with the length of the bond in Å.They are calculated by the HBPLUS program which computes all possible positions for hydrogen atoms, H, attached to donor atoms, D, which satisfy specified geometrical criteria with any acceptor atoms, A, in the vicinity. The criteria used here are that the H-A distance <2.7Å, the D-A distance <3.3Å, the D-H-A angle >90°, and that the H-A-AA angle >90°, where the AA atom is the one atached to the acceptor, usually preceding it along the amino acid chain.
Protein residues that make one or more non-bonded contacts to the ligand are shown as dark red "eyelashes" whose spokes point in the general direction of the contacted atom. The ligand atoms involved in these contacts also have spokes pointing back.
Here non-bonded contacts are defined as any contacts between ligand and protein involving either a carbon or a sulphur atom, where the interaction distance is ≤3.9Å. These interactions are also computed by HBPLUS.
Further information about LIGPLOT can be found at:-