PLIP - Quick Tutorial

This tutorial will show you how to search for a protein-ligand complex of interest using the PDB wizard, run an analysis with PLIP as well as how to view and interpret the results.

Usage

Searching using the PDB wizard.

Open the main page of PLIP. Here, you have three different options to choose a structure to be processed, either by uploading a protein-ligand complex in PDB format, providing a PDB ID, or by searching for PDB entries with the wizard. For this quick tutorial, we will use the wizard to search for structures of RNA editing ligase. Click on the little magnifier icon or the text 'Search for PDB-structures' right to the input field for PDB IDs. In the protein search field type in RNA editing ligase (A) and click on Search. As shown in the result list, the PDB entry 1XDN (RNA editing ligase 1 from Trypanosoma brucei) is the only match containing a structure with a ligand for this search (B). Click on 1XDN from the result list, the identifier will be automatically copied into the PDB ID search field. Now, click on Run Analysis to start the analysis. As soon as the calculation has finished, you will be redirected to the results page.

Results

Interpreting the results.

On the results page, PLIP lists all interaction data, grouped by ligand type (Small Molecules, DNA/RNA, Ions, Polymers), and eventually single complexes. The given structure contains only one complex with ATP and a magnesium ion. Now, expand SMALLMOLECULE+ION, then ATP, and finally click on the entry for the protein-ligand complex ATP-A-501 (Adenosine Triphosphate) to show the interaction details (C).

PLIP has detected mainly hydrogen bonds, water bridges and salt bridges for this complex. There is, however, one prominent π-stacking interaction and a complexation of the magnesium ion between water and ATP. At the top of the entry, a rendered image gives you an overview on the contacts. You can check the details for each single interaction in the tables below the visualization. To see which amino acid participates in the stacking, scroll down to the table π-Stacking (E). You can see the explanation for each attribute in the mouseover text. In this case, a phenylalanine residue makes contact with an aromatic ring of ATP adenine. As indicated in the title of table and the legend of the rendered image on the top, π-stacking interactions are indicated by green dashed lines. Click on the red button titled Click for 3D-View to start a JSmol applet, giving you more information on interactions and labels to quickly identify and explore interactions in the structure.

Generating figures for talks or publications

Generating images using PyMOL.

In case you need a higher-resolution picture than provided or want to show the protein-ligand complex from a different angle, you can download the corresponding PyMOL session file via the link provided below the image (D). Let's prepare an image of the ligase-ATP complex with focus on the stacking interaction. Double-click on the pse file or open PyMOL and choose File -> Open. Click and hold the left mouse button and move the molecule until you get a good view on the stacking (F). Let's say we are not interested in water bridges for our purpose. You can hide any interaction type via the named groups on the right side menu. To hide all water bridges, expand Interactions, then click on WaterBridges (G). Hiding the water molecules can be done via accessing .Other and then (H)ide everything for the (Water) selection (H). To render an image, it is recommended to ray-trace (type ray and press Enter) before exporting from PyMOL. To save the file, choose File -> Save Image as -> PNG.