Transcript The Protein Data Bank (PDB) & PDB Files

The Protein Data Bank (PDB)
& PDB Files
Lesson Date: 09/01/04 – W
Created by: Angela M. Amoia 08/20/04
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
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
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!
Contents of PDB file
General information about the molecule:
name, ligands, sequence, references to journal articles, etc.
Contents of PDB file
Information about each atom in the structure:
arranged in sequence- first amino acid first, last amino acid last
Atom Name
Atom Number
Chain
Residue Name
Atom Type
Residue Number
Temperature Factor
Position - (XYZ Coordinates)
Occupancy
ATOM - indicates this line contains atom coordinates
ANISOU - if your file contains this line, don’t worry about it!
How can I obtain PDB files
associated with an article?
(1) Link from PubMed article to associated
structures in PDB
(2) Directly from PDB using the PDB
accession number acquired from a paper
If I already have a structure in
mind, how can I find articles
associated with it?
(1) Use the PDB search engine and link
from the PDB to PubMed
Shall we…