Analyze the Data 3-1: The Protein Data Bank
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."
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