Basic Applied Bioinformatics

CHAPTER 3Downloading Protein Structure

CS Mukhopadhyay and RK Choudhary

School of Animal Biotechnology, GADVASU, Ludhiana

3.1 INTRODUCTION

The tertiary structure of a protein can be downloaded from the Research Collaboratory for Structural Bioinformatics Protein Databank (RCSB‐PDB). It is a repository for the three‐dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is managed by the Worldwide Protein Data Bank (wwPDB).

3.2 OBJECTIVE

To download the structure of taurine beta‐lactoglobulin peptide from the protein databank (PDB).

3.3 PROCEDURE

1. Open RCSB‐PDB: http://www.rcsb.org/pdb/home/home.do
2. Enter the name (or sequence or ID) of the target protein in the search text box provided at the top of the page. In this example, it is <Beta‐lactoglobulin AND “Bos taurus”> (Figure 3.1).
3. One can further filter the search results by clicking on “Refine Search”. This process will narrow down the search, based on the following classifications: “IDs and Keywords,” “Structure Annotations,” “Structure Features,” “Deposition,” “Chemical Components,” and so on.
4. Click on “Unliganded form of bovine beta‐lactoglobulin, ambient pressure” to get the structure of the target protein (Figure 3.2).
5. Download the protein structure in PDB file format. This is a file format where the file has a *.pdb extension.
6. The three‐dimensional image can be viewed by clicking on the “3D View”. Java^TM must be installed in the system to view the 3D image (Figure ...