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• Switch (parts of) each binding site on and off.
• Colour the (various parts of) each binding site separately.
• View H-bond or short range interactions.
• There are two distinct binding modes depending on the type of ligand. Find out what
characterises these two binding modes. Look at the positions of the water molecules to help find
these.
• Investigate the results shown in the analysis of superimposed chains summary table. Investigate
how flexible the main and side chains are. Are there any conserved water molecules in the
binding site? Consider changing the reference by selecting the Change Reference Chain button
and select the Recalculate Table button to create a new table.
1.7 Investigating Crystal Packing Effects
superposition of binding sites can be carried out including crystal packing effects, thus allowing
investigation of the influence of crystal packing on the ligand binding mode, within a series of related
structures.
The aim of this example is to search for crystal packing effects in factor Xa binding sites and find out
which structures are influenced by crystal packing effects:
• Click on the Text Search button in the Relibase+ menubar.
• Type 1fax into the Search String box, ensuring the Search Type menu is set to PDB Entry-Code
Search, then hit the Submit button.
• Go to the Ligand Information page for DX9 in the retrieved PDB entry for 1fax and click on the
Similar Binding Sites Search button as in the previous example.
• In the resulting page accept the default values and start the search for similar chains by clicking
on the Submit button.
• In the options which are available for chain selection click on With Ligands Only, which will
exclude entries with no ligands from your current selection.
• Since you want to investigate crystal packing for these similar binding sites ensure that the Get
Crystallographic Environment check box is selected; Packing tick boxes will then be present in
the Hermes Protein Explorer.
• Click on the Submit button to superimpose the selected chains.
• Use Hermes to have a detailed look at all components of the various superimposed complexes.
As the Get Crystallographic Environment check box was selected there is an additional column
of Packing check boxes which allow you to switch the crystal packing of the protein-ligand
binding sites on and off. If there are no check boxes this indicates crystal packing isn’t available.
• If you select 1xka you will see that packing residues (Lysine side chains) bind in the S4
specificity pocket which is filled up by parts of the ligand in all other superimposed structures in
Relibase+ User Guide
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