10. Explore the structure of γ-crystalline (4GCR in pdb).
All the questions to this problem can be answered using resources provided in or linked to the protein data bank at www.rcsb.org/pdb/
Search for the structure for γ-crystalline (4GCR).
Display the PDB file.
How many residues does this enzyme have?
How many water molecules are associated with the enzyme in the crystal structure?
Draw skeletal diagrams of Glu and Tyr and label their atoms using the same nomenclature employed in the PDB file.
What are the atomic coordinates of the S atom of Cys 32?
View the structure using Jmol.
right-mouse click on Jmol to get access to additional Jmol functionality and see if you can color the cartoon diagram by secondary structure.
Is the protein primarily helical or sheet?
How many subunits does the protein have?
How many domains?
Return to the main page.
Select the Links Tab.
Scoll down to STRUCTURE CLASSIFICATION AND COMPARISON
How do CATH and SCOP classify the structure of this protein?
Enter the following information
PDB identifier: 4GCR Chain: A
Do a structural alignment and a 3D structural comparison of GCR to1ELP-A (Gamma D crystallin)
Repeat for Carbohydrate binding protein (3HZB-A)
How do the structures compare?
What is the sequence identity between the proteins?
What is the RMSD for the alignment?