Protein Database and Protein Visualization Lecture

Class Materials


1.Take a photo of physical model of the four helix bundle cytochrome b562, PDBID: 256b. Browse Protein structures in and if possible make your physical model and take picture 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 poster of the structure from Nishimasu H, et al.’s CRISPR-Cas9 paper (Source:

Please email the dropbox/google drive link to your homework to me by April 3, 2020

The homework is nested in your own directory called YourID_YourFirstName/ and put these files in there.




Returned Homeworks

Physical Models


CRISPR-Cas9 poster