Structural Bioinformatics
Assignment 1
The objective of this assignment is to familiarize you with protein structure.
Please follow the instructions below, and send the resulting PNG image to my email
avraham.samson@biu.ac.il
with "Structural Bioinformatics - Assignment 1" in the title.
Answer the question in the body of the email.
1. In a web browser, go to the PDB at www.rcsb.org,
and download the structure of 1GSA (glutathione synthetase)
2. In PyMol, open the structure 1GSA (or any other molecular viewer of your choice).
3. Click on the "Display"->"Sequence" to show the protein sequence, and heteroatoms.
Glutathione transferase catalyzes the condensation of gamma-glutamylcysteine and glycine, to form glutathione (GSH).
The catalytic site contains two magnesium ions (MG), and ADP. The enzyme is surrounded by several water molecules (O).
4. Click "H"->"Waters" and hide all water molecules.
5. In the sequence, select the ADP and GSH, and display them as sticks by clicking Select->"S"->"Sticks"
Color ADP, and GSH in element colors by clicking Select->"C"->"By Element"=>"CHNOS".
6. Select the two MG ions, and display as spheres, by clicking on Select->"S"->"Spheres", and color magenta by clicking Select->"C"->"Magenta".
7. Select the protein chain, and color according to secondary structure elements by clicking Select->"C"->"By SS"->"Helix Sheet Loop".
8. Change background to white by clicking on "Display"->"Background"->"White".
9. Save image by clicking on "File"->Export image"->"PNG", and attach it to the email.
Question 1. Measure the distance between the two MG ions by clicking "Wizard"->"Measurement" and write the answer
in the email body. In one sentence, please explain how you would calculate this distance based
on the following XYZ Cartesian coordinates?
MG319:
x=22.61Å y=19.09Å z=73.759Å
MG320:
x=22.05Å y=18.82Å z=70.201Å