Protein Structure Database (PDB)

Protein Structure Database (PDB)

Introduction

The Protein Structure Database (PDB) is the primary global repository for the three-dimensional (3D) structures of biological macromolecules such as proteins, nucleic acids, and protein–ligand complexes.

These structures are determined experimentally using techniques like X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, and Cryo-Electron Microscopy (Cryo-EM).

PDB plays a vital role in understanding:

Protein structure and function

Molecular interactions

Drug discovery and design

Structural biology and bioinformatics

History and Development

Established in 1971

Founded by Brookhaven National Laboratory (USA)

Initially contained only 7 protein structures

Now maintained by the Worldwide Protein Data Bank (wwPDB)

Members of wwPDB

RCSB PDB (USA)

PDBe (Europe)

PDBj (Japan)

BMRB (Biological Magnetic Resonance Data Bank)

Objectives of PDB

To collect, store, and distribute 3D structural data of biomolecules

To provide free and open access to structural information

To ensure standardization and validation of structural data

To support research and education worldwide

Types of Molecules Stored in PDB

Proteins

Enzymes

Nucleic acids (DNA, RNA)

Protein–protein complexes

Protein–ligand and protein–drug complexes

Virus capsids and ribosomes.

Experimental Methods Used

1. X-ray Crystallography

Most common method

Requires protein crystallization

Provides high-resolution structures

2. NMR Spectroscopy

Used for small proteins

Structure determined in solution

Multiple conformations possible

3. Cryo-Electron Microscopy (Cryo-EM)

Suitable for large complexes

No need for crystallization

Rapidly growing method

PDB File Format

Each structure in PDB is assigned a unique 4-character PDB ID (e.g., 1ABC).

Main Components of a PDB File

HEADER – General information

TITLE – Description of the structure

EXPDTA – Experimental method

ATOM – Atomic coordinates

HETATM – Non-standard atoms (ligands, ions)

SEQRES – Amino acid sequence

CONECT – Bond connectivity

END – End of file

Data Organization in PDB

Primary structure: Amino acid sequence

Secondary structure: α-helices, β-sheets

Tertiary structure: 3D folding

Quaternary structure: Multisubunit assembly

Structural Validation in PDB

Before acceptance, each structure undergoes quality checks:

Resolution assessment

Ramachandran plot analysis

Bond length and angle validation

Steric clash detection

Validation reports are available for each PDB entry.

Access and Tools Provided by PDB

Structure visualization (3D viewers)

Sequence and structure search tools

Structure comparison

Download options in multiple formats

Educational resources.

Applications of PDB

1. Structural Biology

Understanding protein folding

Studying structure–function relationships

2. Drug Discovery

Structure-based drug design

Identification of drug binding sites

3. Bioinformatics

Homology modeling

Molecular docking studies

Protein classification

4. Medical and Clinical Research

Studying disease-related mutations

Designing therapeutic proteins

5. Education

Teaching protein structure and function

Training students in molecular biology

Advantages of PDB

Free and open access

High-quality curated data

Global collaboration

Supports advanced computational analysis

Limitations of PDB

Not all proteins have known structures

Some structures have low resolution

Static structures may not reflect dynamic behavior

Importance of PDB in Modern Biology

PDB acts as a bridge between sequence and function, helping scientists understand how molecular structure determines biological activity. It is an indispensable resource in genomics, proteomics, drug discovery, and biotechnology.

Conclusion

The Protein Structure Database (PDB) is the world’s most important repository for 3D macromolecular structures. By providing reliable and accessible structural data, PDB supports research in biology, medicine, and bioinformatics, making it a cornerstone of modern life sciences.

Comments

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