The Protein Data Bank (PDB) & PDB Files

1. The Protein Data Bank (PDB) & PDB Files Lesson Date: 09/01/04 – W Created by: Angela M. Amoia 08/20/04

2. Lesson Objectives • Recall what the PDB is and what is stores • Recall what a PDB file is and what its contents stand for • Summarize two (2) ways to obtain PDB files associated with an article • Summarize how to find articles associated with a PDB file

3. Protein Data Bank (PDB) • Single World Wide database • Stores atomic coordinates of protein & nucleic acid structures known • Coordinates determined by: • X-Ray Crystallography • NMR • Assigned ‘PDB ID’ or ‘accession number’ • 4 characters; ex. 1ANG

4. PDB File (.pdb) • Text file, viewed/modified in editor (TextPad) • a.k.a. structure file • Contains position of every atom in the file as well as some information about the structure • Holds all the information needed to reconstruct a 3D model of a molecule – view in RASMOL or DeepView • At first, contents are intimidating! But they are actually quite simple documents!

5. Contents of PDB file General information about the molecule: name, ligands, sequence, references to journal articles, etc.

6. Contents of PDB file Information about each atom in the structure:arranged in sequence- first amino acid first, last amino acid last

7. Atom Name Chain Atom Type Atom Number Residue Name Residue Number Temperature Factor Position - (XYZ Coordinates) Occupancy ATOM - indicates this line contains atom coordinatesANISOU - if your file contains this line, don’t worry about it!

8. How can I obtain PDB filesassociated with an article? • Link from PubMed article to associated structures in PDB • Directly from PDB using the PDB accession number acquired from a paper

9. If I already have a structure in mind, how can I find articles associated with it? • Use the PDB search engine and link from the PDB to PubMed

10. Shall we…