Find the PubChem Compound Summary page for aspirin
Find a protein structure of PLA2 containing bound aspirin
Align the PLA2-aspirin complex with a PLA2-tylenol complex
Identify residues important for the binding of aspirin and tylenol
Steps
Retrieve the PubChem Compound Summary page for aspirin
On the NCBI home page, enter aspirin[completesynonym] in the search box and click Go.
Find the PubChem Compound results and click on the number of hits, and then on the CID (Compound IDentifier) for the
first record retrieved.
Find a 3D structure containing aspirin bound to PLA2
Click on the link to the right of Protein Structures.
Click on accession 1OXR, a 1.9A structure of a PLA2-aspirin complex.
View the complex in Cn3D
Take a moment to locate the protein chain and ligands on the structure summary page. What other ligand is present
besides aspirin? (Hint: click the magnifying glass or the ligand itself; simply doing a "mouse-over" of the
ligand will also work.)
Click View 3D Structure to launch Cn3D.
Import a PLA2-tylenol complex
In the Sequence/Alignment window of Cn3D, choose Show Imports from the Imports menu.
In the Import Viewer window, choose Import Structure from the Edit menu.
Select Via Network, click OK.
Enter 39216 (the MMDB-ID of PDB record 2DPZ) and click OK.
The imported structure contains its structural alignment (using VAST) to 1OXR.
View the structural alignment of the two complexes
In the Import Viewer window, choose Merge All from the Alignments menu. Both structures are now in the Sequence/Alignment viewer.
Close the Import Viewer.
To view the structural alignment, we need to save and reload this file. In the Structure window, choose Save As... from the File menu, and give the file a name. Save with format
Binary ASN1.
Now choose Open from the File menu, and open the file you just
saved. You should now see two aligned structures.
Locate binding site residues in the two complexes
In the Structure window Style menu, choose Coloring Shortcuts and
then Object. This colors the two structures differently (see the Sequence/Alignment window to
tell which one is which).
Double-click on each of the two Aspirin and Tylenol ligands to select them (turn them yellow).
In the Structure window Show/Hide menu, choose Select by Distance and
then Residues Only. Enter a radius of 3.25A and click OK.
Amino acids with atoms within 3.25A of the two ligands will be highlighted in yellow in both the Structure and
Sequence/Alignment windows. Compare the yellow letters in the Sequence/Alignment window to identify binding differences.
