ProblemSet1key_002 bibc 100

ProblemSet1key_002 bibc 100 - BIBC 100 Problem Set #1...

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BIBC 100 Problem Set #1 4/11/08 1) Go to the PDB website (Protein Data Bank), and retrieve PDB ID “2cpl”. See the “Images and Visualization” box to the right. The programs KiNG, Jmol, Webmol, etc. allow you to look at the structure of this protein and manipulate it in various ways. You will have to experiment with the various programs and see what they do. I find KiNG and Webmol to be the easiest to understand; Jmol isn’t too bad either. All require Java – I ran these programs in the Safari browser, with the Mac OS X operating system. I expect this exercise to take you about 2 hours to complete. What is this protein? What does it do? cyclophilin A, it is an enzyme (isomerase: peptidyl prolyl cis-trans) Is this protein made up of a single amino acid chain, or multiple chains? How long are the chain(s)? One chain, 164 amino acids Describe the secondary structural composition and any major folds/motifs you see in this protein. eight-strand beta sandwich (beta barrel) motif, flanked by two alpha helices
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ProblemSet1key_002 bibc 100 - BIBC 100 Problem Set #1...

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