Protein Data Bank

Introduction

In order to view a protein molecule using Jmol, you need to have a 3-dimensional structure file. These files contain the (X,Y,Z) coordinates for the atoms that make up a structure, along with information about each atom.

The most common file formats used with Jmol are Protein Databank (.PDB) files and MDL Molfile (.mol) files. Today we will only be using .PDB files.

What is the Protein Databank?

The protein data bank is an archive of 3D shapes of proteins, nucleic acids, and complex biology structures that helps students and researchers understand all aspects of microbiology. The protein data bank is the primary source for large protein structure files, and currently contains over 100,000 structure files on the www.rcsb.org website.

For information on how these structure files are determined visit:

http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction

For information on understanding these structure files visit:

http://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/methods-for-determining-structure

Finding Structures on the Protein Databank

Each structure on the Protein Databank has a unique four character long alpha-numeric identifier, known as the PDB ID.

Often more than one .pdb file exists for a specific type of protein. For example, there are hundred of .pdb file entries for the relatively common protein Hemoglobin. It is often a good idea to use specific information about a structure listed below to help determine if you have found the best possible file.

Who are the authors of the PDB file?
In which journal was the primary citation published?
On what date was the file deposited into the PDB?
How many chains are in this file?
Are there any heterologous groups within this PDB file? If so, which ones?
From was source was this molecule isolated?

The Structure Summary Page

When you click on a specific PDB ID, you will see the Structure Summary page for the structure. This page includes a wealth of information in the following order:

PDB Structure ID Number
Title
Classification (Type of Molecule)
Source (Organism it is from)
Authors
Primary Citation
Macromolecules
Small Molecules
Experimental Data & Validation
Entry History
Molecular Description
Functional Class
Source of the Molecule
Chemical Component

The Sequence Page

When you click on a specific PDB ID, it automatically brings you to the structure summary page. To find the sequence page, click on the sequence tab at the top of the page.

This page will give the amino sequence of each chain and show where secondary structures can be found.