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Ligands and metals

Any unique ligands and metals in the structure have their own page. An example is given below.

a. Thumbnail image 
b. Ligands
c. Metals
d. Ligand molecule
e. LIGPLOT
  Ligand/metal page

a-c. Thumbnail image, list of ligands and list of metals

The left-hand side of the ligands/metals page is similar to the top page and is as shown below.

a.
b.
c.
 

a. Thumbnail image

Where the ligand/metal is not the only molecule in the structure the thumbnail image(s), rendered using Raster3D, shows all copies of the current ligands/metal in the structure in solid spacefill while rendering all other molecules as transparent. This is to provide an indication of their location in the overall structure.

 

b. Ligands The first tree shows the full list of ligands with the current one highlighted. (In this example, there is only a single ligand in the structure). Each unique instance of a ligand is shown. Thus if, say, a structure contains 4 instance of the same ligand, bound to identical protein chains, only one instance of the ligand will be represented by its own ligand page.

 

c. Metals The second tree shows the full list of metals. As for ligands, only unique instances of each ligand are represented.

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.

e. LIGPLOT

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

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.

Non-bonded contacts

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:-

http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT spacer
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