Using the Protein Data Bank
updated 22/05/02

Return to Immunology Exercises

In this exercise your are expected to:

• Access the Protein Data Bank
• Use PDB ID codes
• Search the Protein Data Bank for specific proteins
• Interpret Summary Information about the protein
• Interpret Sequence Details about the protein
• Download files in PDB format from Protein Data Bank
• Submit a report that answers the questions in the exercise to the  COURSE ASSIGNMENT DATABASE

Access to Protein Data Bank

The Protein Dank Bank is an international repository of data on the structure of proteins Researchers from around the world deposit their information here so that it can be used by the scientific community.

Data on thousands of proteins are stored in separate files each with a unique four letter PDB identification code

The Protein Data Bank is constantly updated and modified as they find faster ways to retrieve the information. Do not be surprised if the screen layout changes frequently as improvements are brought online.

As you browse the PDB website look for answers to the following questions

SUBMIT YOUR ANSWERS TO THE COURSE ASSIGNMENT DATABASE

• What is the function of the PDB
• What organizations support the PDB
• What kind of information is stored in the PDB
• What methods are used to generated 3D structural data?
• What are some of the limitations of X-ray crystal diffraction
• What are the advantages of NMR?
• What are the limitations of NMR?
• How many 3d structures are currently on deposit with the PDB?

	Click on the logo to access the data bank and find the answers to the questions
Protein Data Bank Home page

PDB ID codes

Each file is stored with a unique four digit code that is a combination of numbers and letters e.g. 1KEL, 1CD8 etc.

If the file name looks like ***.PDB then the info is stored in a special format that can be read by several graphics programs, such as RasMol, and word processors. You can open these files, read them and save them to your computer for use by RasMol

Searching the Protein Data Bank

SEARCHLITE

All the data files are stored with a PDB ID. If you know the code this is the fastest way to get the data. Most of us do not remember these codes as there are thousands of different files

The easiest search method is a keyword search of the entire database The keyword, may be the name of molecule, the name of the author who first published the information, the method used or even the PDB ID. The search will return a list of all the files that contain the keyword. The keyword Lysozyme returns a list and a brief description of over 650 files. You select a file and explore it until you found the one that you need. Alternatively you can narrow your search by combining Keywords using Boolean logic.

You can get a lot of information quickly by using the Summary Information Page and the Sequence Details Page

Go to the Protein Data Bank Home page , select the SearchLite option and start a search as follows

1: Enter keywords known to relate to the biological macromolecules of interest (e.g. lysozyme) in the key word window
2: Start the Search Select the "Search" button or "Enter" on your keyboard (PDB is an extremely busy, very large, site, it may take some time for the information to load or you may have to try a few times before accessing the information)
3: Select a file from the list ( use the check off box on the left of the screen)
4; Read the file: Click on the Explore option to activate the Structure Explorer
5: Find the Summary information for the file and answer the following questions

SUBMIT YOUR ANSWERS TO THE COURSE ASSIGNMENT DATABASE

• What is the PDB ID code?
• what is the name of the protein?
• What organism produced the protein?
• How many amino acids are there, and in what sequence?
• How many polypeptide chains? The names of the chains?
• How many atoms are there?
• Are there any additional hetero atoms involved? (what is a hetero atom?)
• Where was the data originally published?
• Who were the authors of the original manuscript?
• What method was used to obtain the 3D coordinates ( X-ray, NMR, Theoretical)

6: Find the Sequence Details section and answer the following questions

SUBMIT YOUR ANSWERS TO THE COURSE ASSIGNMENT DATABASE

• How many polypeptide chains are there?
• What is the identification name for each chain?
• How many residues (amino acids or nucleotides) are there
• How many alpha Helices?
• How many Beta Sheets?

7: Download the file to your computer using the Download/Display File option

IMPORTANT!!! 

YOU WILL USE THE DOWNLOADED FILES IN LATER EXERCISES SO BE SURE THAT YOU HAVE MASTERED THIS SKILL

• go to the table entitled Download the Structure File
• select the PDB format with no compression.
• remember the name of the file. the four digit file identification code and the extension.
• remember where you stored the file
• Remember the format of the file

RESOURCES:

Protein Database : database for 3D protein structures

Rasmol Home Page : excellent viewer for those protein structures found in the Brookhaven Protein Database, contains different versions of Rasmol for Windows 3.1, Windows 95 Unix, Macs etc. instructions tips updates etc

Swiss Protein Sequence Database :database for protein sequences Go to the resources section of the course website and download Protein Database files for B cell receptors and epitopes