Structural Databases

[Slides]

Assignments

1.Take a photo of physical model of the four helix bundle cytochrome b562, PDBID: 256b, with your name written underneath.

2.(a) How many hemoglobin structures that cause sickle cell anemia (hemoglobin S) are deposited in the PDB?   (b)What is the part of the protein (buried/surface) that this amino acid mutation occurs? (c) Discuss why normal hemoglobin (Glu 7, Asp73) is less likely to form fibers than Hemoglobin C-Harlem (D73N, Chain B + E7V, Chain H).

3.(a)How many CDK kinases with resolution < 1.5Å are deposited in the PDB? (b)Send me a picture of the CDK-ligand interaction, tell which PDB code you have got it from.

4.Learn to create GIF animation or poster of the structure from Nishimasu H, et al.’s CRISPR-Cas9 paper (Source: http://www.sciencedirect.com/science/article/pii/S0092867414001561)

5.(a)Go to MANORAA.org, click on Sample page under the logo, explain how the amount of hydrogen bonds + ionic interaction and structural conservation might be useful for drug design. (b)Pick one drug and make an all English infographic chart of the drug’s target protein, pathways, human organ, expression levels and, if available,SNPs.

Please email the link to homework to duangrudee.tan@mahidol.edu

Directory YourID_YourFirstName/

1)YourName_practical.pdf

2)YourName_physicalmodel.jpg

3)YourName_CRISPR.png/gif

4)YourName_YourDrug.pptx (You can download example template here! )

 

 

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