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Comparative Analysis of Structures 1NXB and 5EBX

Analyze the differences in relative geometry and biological aspects of structures 1NXB and 5EBX. Investigate the sequence, identify any discrepancies, and determine if one structure is incorrect. Utilize PDB validation server, PDB geometry tab, Whatif reports, PDBsum, and Procheck for evaluation.

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Comparative Analysis of Structures 1NXB and 5EBX

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  1. Assignment 2 – Due 10/17/12 • The objective is to ascertain as much as you can from a comparative analysis of structures 1NXB and 5EBX. In so doing address the following questions: • What are the differences in relative geometry of the structures? For each geometric feature give a brief explanation of what that feature means • What do you notice about the sequence of the two structures? What has happened here? • What are the biological differences between the structures if any? • Are these truly different structures or is one wrong? If so which one?

  2. Use and Document Your Use of at least the Following Resources • PDB validation server http://deposit.pdb.org/validate/ • The PDB geometry tab for each structure • Whatif reports http://swift.cmbi.ru.nl/servers/html/index.html • PDBsum http://www.ebi.ac.uk/pdbsum/ and Procheck which is part of it • Additional points for use of resources you find

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