How do I show the sequence conservation around the ligand binding site?
Here is an example of how to superimpose the structures of two proteins and display the sequence conservation around the ligand binding pocket. PDB Search • PDB Search Tab 1ql6 • PDB Search Tab 1ian • Select both receptors by double clicking on the name of the receptor in the ICM Workspace. To select two receptors use the Ctrl button or use the shift button to select a range of objects in the ICM Workspace. A receptor which is selected will be highlighted in blue in the ICM Workspace and with green crosses in the graphical display. • Superimpose both structures by clicking on the display tab and selecting the superimpose button. • Now that the structures are superimposed we can unselect everything – to do this right click and drag in blank space in the graphical display or double click in white space in the ICM Workspace or use the unselect button green box with red cross through it. • Now extract the sequence information from each protein. To do this right click on the molecule “a” of
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