Step-by-Step Guide to Using PDB

Step-by-Step Guide to Using PDB

Step 1: Access the Website

Go to www.rcsb.org (Figure 1).

Figure 1: The Protein Data Bank and How to Search for Your Target Protein. 

Step 2: Search for Your Target Protein

• In the search bar, type the protein name (e.g., “HIV protease”) (Figure 1).

• Example: Searching "EGFR kinase domain" retrieves multiple structures.

Step 3: Review Search Results

• Each entry has a PDB ID (a four-character alphanumeric code, e.g., 1TW7) (Figure 2).

• Check resolution (smaller = better), experimental method (X-ray, cryo-EM), and whether ligands are bound.

Step 4: Explore the Protein Structure

• Click on a structure to open its detailed page (Figure 2).

• You’ll see:

  • 3D View (interactive model).

  • Experimental Details (resolution, authors, publication).

Figure2: Explore the Protein Structure

Step 5: Download the Structure

• Use the Download Files option (Figure 3).

• Choose PDB format (for docking, visualization) or mmCIF format (for advanced analysis).

Figure 3: Fetching the PDB structure from the protein data bank

When looking at a PDB entry for drug design, you should look at a few important pieces of information:

Resolution: In crystallography, resolution tells you how good the data is. Higher resolution (a lower number) usually gives more accurate atomic positions.

R-values: R-work and R-free show how well the atomic model fits the data from the experiment. Lower values show a better fit.

Completeness: The ratio of actual data to theoretically possible data.

Coverage: The amount of the biological macromolecule that is shown in the structure.

Selecting the right protein target and obtaining its high-quality structural information from the PDB are crucial first steps in computer-aided drug design. By understanding the disease biology and effectively utilizing the PDB, researchers can lay a strong foundation for the rational design and development of novel therapeutics.

REFERENCES

Berman, H. M. (2000). The Protein Data Bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235.

Guterres, H., & Im, W. (2020). Improving Protein-Ligand Docking Results with High-Throughput Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 60(4), 2189–2198. https://doi.org/10.1021/acs.jcim.0c00057

Nelson, D. L., Cox, M. M. (2017). Lehninger Principles of Biochemistry (7th ed.). W. H. Freeman. 

RCSB PDB (2023). PDB-101: Learn Guide to Understanding PDB Data. https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction

RCSB Protein Data Bank. (2025). https://www.rcsb.org