Retrieval and Analysis of Protein Structural Data using PDB – B.Sc. Bioinformatics Practical

 

Retrieval and Analysis of Protein Structural Data using PDB – B.Sc. Bioinformatics Practical

Aim of the Experiment

To retrieve and study the three-dimensional (3D) structure of a protein from the Protein Data Bank (PDB) and visualize its structural features.

Principle

The Protein Data Bank (PDB) is a global repository that stores experimentally determined 3D structures of proteins, nucleic acids, and complexes.

• Structures are obtained using:
  • X-ray crystallography
  • NMR spectroscopy
  • Cryo-electron microscopy
• Each structure has a unique PDB ID
• Data includes atomic coordinates, secondary structures, and ligands

The database is maintained by the RCSB Protein Data Bank.

Requirements

• Computer with internet connection
• Web browser
• Access to RCSB Protein Data Bank
• Visualization software (optional):
  • PyMOL
  • UCSF Chimera

Step-by-Step Procedure

Step 1: Open PDB Website

• Go to RCSB Protein Data Bank
• You will see a search bar on the homepage

Step 2: Enter Search Query

• Type:
  • Protein name (e.g., Hemoglobin)
  • Enzyme name
  • Or PDB ID (e.g., 1A3N)

 Example: Hemoglobin Homo sapiens

Step 3: Run Search

• Click Search
• A list of protein structures will appear

Step 4: Select a Structure

• Click on a suitable entry
• Check:
  • Resolution
  • Method (X-ray, NMR, Cryo-EM)
  • Organism

Step 5: View Structure Summary

• Observe:
  • PDB ID
  • Protein name
  • Authors
  • Experimental method
  • Structure resolution

Step 6: Visualize 3D Structure

• Use built-in viewer on PDB site
• Rotate, zoom, and explore:
  • Alpha helices
  • Beta sheets
  • Ligands

Typical Protein Structure Visualization

6

Step 7: Download Structure File

• Click Download Files
• Choose format:
  • PDB format (.pdb)
  • mmCIF format

Step 8: Open in Visualization Software (Optional)

• Load file in:
  • PyMOL
  • UCSF Chimera
• Analyze:
  • Chain structure
  • Binding sites
  • Molecular interactions

Step 9: Analyze Structural Features

• Identify:
  • Primary structure (sequence)
  • Secondary structure (α-helix, β-sheet)
  • Tertiary structure (3D folding)
  • Quaternary structure (multi-chain proteins)

Step 10: Record Observations

• Note:
  • PDB ID
  • Protein name
  • Organism
  • Structure type
  • Key features (helix, sheet, ligands)

Result

Protein 3D structure successfully retrieved and analyzed from PDB, including identification of structural elements and functional regions.

Precautions

• Choose structures with good resolution (< 3 Å preferred)
• Verify organism and protein function
• Use reliable visualization tools
• Avoid incomplete or low-quality structures

Applications

• Drug design and discovery
• Protein engineering
• Functional analysis
• Molecular docking
• Structural biology research

Viva Voce Questions (with Answers)

1. What is PDB?
   A database of 3D biomolecular structures.
2. What is a PDB ID?
   Unique identifier of a structure.
3. Which methods are used to determine structure?
   X-ray crystallography, NMR, Cryo-EM.
4. What is protein tertiary structure?
   3D folding of a polypeptide chain.
5. What is resolution in PDB?
   Measure of structure quality.
6. Name a visualization software.
   PyMOL
7. What are alpha helices?
   Spiral secondary structures.
8. What are beta sheets?
   Sheet-like secondary structures.