Instructions for downloading PDB structural
files for viewing (PC Users):
Many structures have been
recently resolved, and the Protein Data Bank (PDB) at the Research
Collaboratory for Structural Bioinformatics (RCSB) is an excellent source for these
structures. These instruction will
allow you to download the PDB files onto your computer for viewing through the
use of Roger Sayle’s RasMol.
1. You
can search for the desired molecule at the Protein Data Bank in two different
ways. First, it you know the PDB
Identification number enter it into the box on the right side of the page that
says PDB I.D. To do a key word search
mouse click on “Search Lite” which provides a simple key word search.
2. A list of molecules will be returned, in
order of relevance. A brief description
will accompany each of the returned selections. From this you should be able to identify whether the structure is
that which you are searching for. Pay
close attention to the type of molecule (ie. binding, transferase, chaperone …). Also pay attention to the resolution, which gives an idea on the
quality of the picture (resolution is denoted by a distance in angstroms, the
smaller the better the resolution).
3. To select a certain molecule for further
investigation, mouse click on the red Explore icon that is on the right
of each returned entry. This will show
the summary information.
4. We are specifically interested in the
structural information, so mouse click on View Structure that can be
found on the left portion of the screen.
This will give a variety of versions of the structure.
5. We will be using the RasMol program. Right Click of the Rasmol icon, next select Save Target
As. You will then be prompted to
save the program to your hard drive.
Save the file to the same folder as you saved the RasMol program to make
it easier to find. The file is now on
your hard drive and you are ready to view the structure using RasMol.
Viewing a Saved Structure:
6. Open the RasMol program.
7. Select File => Open and select the
structural file (ending in .pdb) that you wish to view. If the structural files were not saved under
the same folder as the RasMol program you may have to search through you hard
drive for the folder that has the information.
When you are ready select the following
link:
Protein Data Bank (PDB) at
the RCSB
You may also try to search
for your protein structure in NCBI’s Entrez Structure Search. Each structural protein on
file in the NCBI Database has a direct link to the corresponding PDB structure
file. Then you can proceed to download the file from PDB.