1. Searching Relibase entries via the BIBLIOGRAPHIC menu
In this part of the tutorial, entries are located using the Text menu. Complexes of
PEPTIDE BINDING PROTEINS with a series of Lys-X-Lys ligands are investigated.
After starting ReliBase, go into the Text menu. Input peptide binding protein into
the KEYWORD SEARCH field and press the Submit button.
The results of the search look like this:
By clicking on the entries in the left frame, more detailed information about the protein-
ligand complexes is displayed on the right. However, we used the given pdb1b05 to continue.
Click on the Launch button in the 3D Visualizer tool box to open a RasMol window and
to display the protein and all of its ligands. While the CPK model reveals the LYS-CYS-LYS
ligand, the pink balls are uranium atoms. Toggle the water on and measure some
distances.
To get further information about one of the ligands, click onto its 2D drawings (in this
case, the first one was used). Simultaneously, the content of the browser window and the one
of the RasMol window is updated.
The search for similar ligands yields several starting points for further
investigations. More interesting in our case is to look for similar binding sites.
Change the entry for Minimum Sequence Identity to 100%, the value of Maximum
Resolution to 2.5. Submit the query.
33 identical sequences are found and displayed together with the ligands, the value for
chain identity and the length of the aligned region. For further evaluation, you may
(de-)select several entries.
Using all of them, we continued by pressing the Superimpose selected chains button.
The final superimposition result is displayed in the RasMol window. The browser window shows
additional information about RMSD values of the aligned chains together with lists of
data for protein movements, indications of clashes of the ligands and water conservations
and displacements.
Switch on all protein chains, ligands and water molecules to get a comprehensive view of the
effects caused by different ligands situated inside the same binding pocket.
Alternatively, you may also start the search in the Text menu with a known three letter code for the ligand or using the name of one of the authors of these entries.
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