Uploaded July 2023 | Updated September 2026, 5 hours ago
In this lesson, KP demonstrates how to display the active site of carbonic anhydrase using the active site amino acid information from a manuscript. We’ll learn how to save and change the renderings of selections in the names panel. Then, we’ll use our selections to identify water molecules that are hydrogen bonding to the active site. Don’t forget to save your work at the end of this lesson—we’ll use the PyMOL file in Lesson 3!
00:00 Introduction and carbonic anhydrase
00:40 Setting up your workspace
01:00 Finding the journal article from the PDB page
01:18 Terminology break
01:42 Saving selections
02:45 Selecting active site residues
05:06 Renderings and Show/Hide Buttons
06:53 Locate and display active site water
08:17 Show/Hide amino acid backbone (main chain)
REFERENCES
• The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
• Dutta, S. and Goodsell, D. 2004. Molecule of the Month: Carbonic Anhydrase doi.org/10.2210/rcsb_pdb/mom_2004_1
• PDB ID: 3uyn
• Elder, I., Fisher, Z., Laipis, P. J., Tu, C., McKenna, R., & Silverman, D. N. (2007). Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. PROTEINS: Structure, Function, and Bioinformatics, 68(1), 337-343.
In this lesson, KP demonstrates how to display the active site of carbonic anhydrase using the active site amino acid information from a manuscript. We’ll learn how to save and change the renderings of selections in the names panel. Then, we’ll use our selections to identify water molecules that are hydrogen bonding to the active site. Don’t forget to save your work at the end of this lesson—we’ll use the PyMOL file in Lesson 3!
00:00 Introduction and carbonic anhydrase
00:40 Setting up your workspace
01:00 Finding the journal article from the PDB page
01:18 Terminology break
01:42 Saving selections
02:45 Selecting active site residues
05:06 Renderings and Show/Hide Buttons
06:53 Locate and display active site water
08:17 Show/Hide amino acid backbone (main chain)
REFERENCES
• The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.
• Dutta, S. and Goodsell, D. 2004. Molecule of the Month: Carbonic Anhydrase doi.org/10.2210/rcsb_pdb/mom_2004_1
• PDB ID: 3uyn
• Elder, I., Fisher, Z., Laipis, P. J., Tu, C., McKenna, R., & Silverman, D. N. (2007). Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. PROTEINS: Structure, Function, and Bioinformatics, 68(1), 337-343.
