s. Go to the PDBsum database and search using the PDB ID of th #3 (make sure you
ID: 229043 • Letter: S
Question
s. Go to the PDBsum database and search using the PDB ID of th #3 (make sure you type/copy the corre "proteins" e molecule you chose in problem ct ID). After you finish exploring the "top" tab, explore the tab. If your molecule has more than one chain, be sure to focus on only the chain or ains that are proteases (for this exercise you can ignore, e.g., any protease inhibitor that may be in complex with your protein) You may also wish to read about the concept of "protein topology" (c.f.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144300 description and http://kinemage.biochemduke.edu/teaching/anatax/index.html for more aesthetically pleasing and illuminating pictures of the "skeletons" of protein structures) before answering the following questions /pdf/10211836.pdf for a a. What is the enzyme class (EC#) of the molecule you selected? (1 pt) b. What is its preferred substrate? (1 pt) Are there any disulfide bonds ("cystine" residues upon hydrolysis) in your protein? What does your answer say about where you would find your protein: inside or outside a cell? (3 pts) c. d. What is the CATH (http://www.cathdb.info; note that clicking on this link might not work: you may need to copy the link to your browser) classification for each domain (even if there is more than one domain, each may have the same classification) in your protein? Note that the CATH classification for each domain (which will be given a domain ID based on a PDB ID) will be formatted as 1.20.30.40 (and indicated as a "Superfamily")? What does "CATH" stand for and what is meant by the term "architecture" and "topology"? You may also wish to compare the CATH classification of your protein's domains with the description of the Pepsin-like fold found in SCOP2 (http://scop2.mrc-Imb.cam.ac.uk/) at htt cop2.mrc-lmb.cam.ac.uk/4002301.html. (4 pts)Explanation / Answer
a)
b)
c)
d)
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