Homology Modeling: Protocols and Concepts 

Class Location: NCI-Library, NCI-Frederick, MD
Date: 04/17/2003
Click here to view the class notes

Exercise1b: Exploring the active site of Pseudomonas 7A Glutaminase-Asparaginase.

  1. Click open the Swiss-PdbViewer (Fig). Preferences >> Network Type in the File Server www.swissmodel.unibas.ch and for port 27000. Click here to see the picture. Note that the "Path of local PDB files" decides on the directory where the Swiss-PDB decides to download/keep the downloaded files. You can change the download location if you want to.
  2. For help at any time, click the question mark looking symbol, HELP
  3. Also click on Preferences >> General ... and uncheck the Show Log File Upon Loading.
  4. Click on File >> import... The Import radio opens up (Figure) . Click and type 1DJO (PDB ID for Glutaminase-Asparaginase) on the Name window, and click on the button PDB file to download the pdb file from the Swiss-Model server. 1DJO will be downloaded to a directory already chosen in the the File >> import... (figure). The structure of Glutaminase-Asparaginase will be displayed on the main screen (figure).
  5. Select >> None
  6. Go to Build >> Add Hs to add hydrogen atoms to the 1DJO.
  7. Click open the control panel by clicking on Window >> Control Panel
  8. From the control panel, we can see that 1DJO has more than one chains, so let us color each one by a different color. Go to Color >> by chains You can also see the contents of the PDB file from Swiss-PDBviewer by clicking on the icon, pdb view.
  9. Let us now add H-bonds by clicking on Tools >> Compute H-bonds
  10. Click and go to the end of the control panel to see the Hetero Groups. Usually the Hetero Groups are listed at the end of the list. We can see that it has two ligands bound to the active sites one on each of the chain. To see the residues which form H-bonds with the ligands, do the following: a) Go the end of the control panel, and select CAB4000 and CAB4001 by left-clicking on the name of the first Heterogroup and drag the mouse to the second one. If you have done this right, you will see both the ligand names in red color. b)Go to Display >> Show H-bond from Selection c) Display >> Show only group with visible H-bonds d) use the zoom button to zoom/center the view.
In this exercise, we will see what are the residues from chain A that are closer and making contacts with chain B. Before we start, let us go to Select >> All to select all the atoms and press Enter key to display all the atoms.
  1. Let us deselect all the atoms by going to Select >> None
  2. Select >>> Groups Close to another Chain In the Diplay Radius pop-up (figure) select Display only Groups that are within , and set 5 Angstroms as a cutoff value. Hit OK to see the selected residues.

To let Swiss-PDBviewer search for prosite patterns, you need to do the following: Go to the web-link, http://us.expasy.org/prosite/psrelnot.html and download the file called "prosite.dat" to the directory under spdbv called usrstuff (for example, c:\temp\spdbv\usrstuff). To do the prosite search, load the sequence and go to Edit >> Search for Prosite Pattern 


Contact Info: Dr. S. Ravichandran 
              Advanced Biomedical Computing Center, 
              NCI-Frederick, 
              Bldg 430, Frederick, MD 21702
              Tel:  301-846-1991 
              Email: sravi@ncifcrf.gov