Teaching enzymology with the Protein Data Bank: From pandemic to Paxlovid

Oct. 19, 2023 | Duration: 1 hr. 39 mins.

RCSB Protein Data Bank is a rich open-access resource for introducing many aspects of protein structure and function into biochemistry courses. In addition to containing more than 200,000 biomacromolecule 3D structures, it also hosts PDB-101 training materials, the Molecule of the Month series and additional resources for exploring enzyme structure–function relationships.

Starting with an example of the SARS-CoV-2 main protease, we demonstrate how to use new PDB tools, notably interactive sequence and structure (1D-3D) views, ligand interactions and exploration of groups of protein to identify trends and understand structure–function relationships more deeply.

The introduction of each tool is followed by hands-on learning exercises and ideas for preparing a lesson plan using another enzyme. Viewers will learn to use PDB resources to create graphically rich, deeply annotated and engaging lessons about enzyme function for their upper-division undergraduate and graduate students and even administrators or funding agencies.


Stephen K. Burley

Stephen K. Burley
Director, RCSB Protein Data Bank; University Professor and Henry Rutgers Chair, Rutgers University

Paul A. Craig

Paul A. Craig
Professor of chemistry and materials science, Rochester Institute of Technology

Shuchismita Dutta

Shuchismita Dutta
Scientific training, education and documentation lead, RCSB Protein Data Bank

Who should watch

  • Faculty members who teach biochemistry courses that involve structure-function relationships at all levels.
  • Graduate students and post-doctoral fellows who are interested in teaching and science communication.

Key takeaways

  • Navigate the RCSB PDB website to visualize each 3D structure and explore various annotations mapped to it.
  • Compare the shapes, interactions and functions of groups of PDB structure with similar sequences and/or similar structures.
  • Use RCSB PDB data, tools and resources to enhance classroom instructions and build lessons for teaching about enzymes.