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4. Database of 3D protein structures
The three dimensional structure of yeast ribosomal protein L30 is known.
We will take a look at the 3D structure of the protein and check if our
previous secondary structure prediction agrees with the experiments. All
3D structures of proteins are stored in the Protein
Data Bank (PDB). All entries in the PDB is identified by a four-letter
code. The PDB code for the yeast ribosomal protein L30 is '1CK2'.
If you don't know the PDB code for a protein, you can click the 'SearchLite'
to search for it.
1. Go to the Protein Data Bank.
Enter the PDB code '1CK2' and press the 'Explore' button.
2. You will see the following window. Click 'Sequence Details' to view
the secondary structure assignment of this protein.
3. Scroll down the window until you see:
4. Your can check the secondary structure of the protein to see if our
previous
prediction agrees with the experiment:
Consider only the Alpha-Helices (H) and Beta-Strands (E):
5. Now we want to look at the structure of this protein. Go to 'View Structure'.
6. Click 'Ribbons (500x500)' to view a still image of the structure. Or
click here if the internet
is too slow.
Can you identify the secondary structure elements of this protein?
7. You can also look at the 3D view by clicking the 'QuickPDB' button.
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