Protein structures & PDB

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All published protein structures are deposited in the Protein Data Bank (PDB) along with the original data used to solve the structure as well as various measures of the structure quality. The PDB project started in 1971 at Brookhaven National Laboratory and in 1998 the Research Collaboratory for Structural Bioinformatics (RCSB) took over the management of the PDB. The first version of PDB contained 7 structures, but has grown rapidly since then and as of February 2014 holds approximately 98,000 structures most of which are proteins and/or nucleic acids. Around 88% of the structures in PDB are solved using x-ray crystallography and the majority of the remaining structures have been solved using nuclear magnetic resonance (NMR) spectroscopy. Statistics of the current holdings of the PDB can be found here.

The exercise

In this exercise we will have a closer look at protein structures and some of their associated data. To study protein structures, you need a molecular viewer. There are several molecular viewers available today, some commercial, some free. Here, we will be using the open-source molecular viewer PyMOL due to its versatility and ease of use and because it is a highly effective tool for making beautiful illustrations of proteins and other molecules.

If you already have PyMOL installed and know how to operate the basic functions in PyMOL, follow the links below to proceed directly to the exercises. The PyMOL quick reference card below lists some useful tips and commands in compact form.

  • EXERCISE 1 - Mandatory
    • Remember to write down the answers to the questions labelled Q1-Q7.
  • EXERCISE 2 - Optional

If you do not have PyMOL installed, go to the PyMOL page and follow the installation instructions. Section 1.2 on the PyMOL page describes the basic operation of PyMOL. The remainder of the page describes some more advanced PyMOL functions and behaviours.

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