a. Beautiful models of macromolecules such as proteins and nucleic acids have been generated from files of atomic coordinates usually obtained from x-ray diffraction of crystallized samples or NMR analysis of the molecules in solution. The Protein Data Bank (PDB) is a publicly accessible repository of macromolecular atomic coordinate files that can be accessed online at http://www.rcsb.org. Access the PDB and familiarize yourself with its home page. How many molecular structures does it contain today? What is the "Molecule of the Month"?
b. Find the structure for the serine protease chymotrypsin by typing the accession code "1ACB" into the search window. This will take you to a page describing the x-ray crystal structure of a complex formed from bovine alpha-chymotrypsin and the small pseudosubstrate inhibitor protein eglin-c. When and in what journal was the study reporting this structural model published?
_feedback: The Journal of Molecular Biology, 1992.
c. Click on the "Display Files" link and select "PDB File." This file is an atomic coordinate (.pdb) file that specifies the relative positions for each atom in this protein complex as determined experimentally by x-ray crystallography. The first several hundred lines contain background information, including the names of the molecules, their natural sources, how they were prepared for the experiment, statistical analysis of the model quality, and bibliographic information. Eventually, you will arrive at a long list of lines that each begin with "ATOM." These are the atomic coordinates, listed by atom number, atom type, amino acid type, and chain number. Each "ATOM" line ends with five numbers representing the atomic position on an x, y, z axis, its "occupancy," and its "thermal factor."
Go back in your browser and click on the "3D View" tab to view the molecular model. Twirl it around in the viewer. Can you identify the protease? The inhibitor protein? Can you find the enzyme's active site? What other observations can you make about serine proteases from the model of this inactivated complex?
