BCH210H : Protein Data Bank - Large Biological Molecules - Biochemistry Assignment Help

Assignment Task :

PDB #s and Protein Visualization 

The Protein Data Bank (PDB) archive is a repository of experimentally determined 3D  structures and information on large biological molecules, including proteins and nucleic  acids. A search using a unique PDB identifier (4 digit alpha-numeric code) will give you  access to the coordinates of its 3D structure and important information about the  protein and how the structure was obtained. Your individual PDB file number will be  assigned through the group function on Quercus. 

In order to analyze protein structures and generate high quality figures for scientific  publication, many additional protein 3D structure visualization tools are available. Swiss PDBViewer, PyMOL and YASARA are some of the tools listed on ExPASy, the SIB Bioinformatics Resource Portal, and iCN3D, an online web-based 3D structure viewing  site. These programs and websites differ slightly in their visualization, modeling and  simulation tools, and some require downloading of the program. Instructions at the end  of the assignment will walk you through the different programs so that you can try them  out to compare the different features.

Accessing your PDB structure: 

Go to the RCSB Protein Data Bank website at www.rcsb.org and search for your protein  using your unique 4 digit alpha-numeric PDB identifier. Your search will generate  information about its structure, a summary of important information and the methods  used to obtain the structure, as well as the citation for how the structure was  documented and published. The “3D View” tab allows you to view the structure and  manipulate it by rotating and displaying some information, however, this format may be limiting when it comes examining the precise interactions within a protein and  understanding the complete structure.

The PyMOL window is split into 3 sections, the External GUI (Graphical User Interface)  along the top, where commands can be entered following ‘PyMOL>’, the main Viewer  window and the Internal GUI on the right. 

1. In the External GUI command prompt line, type: fetch PDB# (where PDB# = PDB file #  alpha code from above) and press enter to load the structure for vts1. Your structure  should have loaded as a cartoon of secondary structure. 

2. In the External GUI command prompt line, type: bg_colour white and press enter to set  the background to white. 

3. On the Internal GUI, click on H=Hide the waters from the structure. 

4. In the bottom right-hand corner click on S. A banner will appear at the top that displays  the amino acid sequence and ligands in your structure. Select your ligand (either in the  banner or in the structure itself). The internal GUI will show (sele) highlighted. Click the  background to deselect. From the menu of (sele), click on S=Show As sticks to display  your ligand as a stick model. You can also change the colour of the (sele) using the  C=color tab. It may also be useful to colour your ligand by element by clicking C=color  by element HNOS.

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