Introduction to the
Protein Data Bank
Learning to Use the RCSB PDB Portal
What is the PDB?
• Archive of experimentally determined (Xray crystallography, NMR, electron
microscopy) 3D structural data
• It contains
– Coordinates of all atoms in the structure
– Macromolecular sequences, experimental details and
links to other biological resources and databases
– Experimental data files used to determine the
structures
• PDB entries have unique alphanumeric IDs
(e.g. PDB ID 1ABC)
Why bother with the PDB?
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Visualize the molecule (or parts of it)
Clues to function
Compare and analyze structure
Understand normal functioning and
disease states
• Design/develop new medicine (diagnostic
procedures, treatments)
The Data Pipeline
Genomic
Based Target
Selection
Isolation,
Expression,
Purification,
Crystallization
Data
Collection
Structure
Determination
PDB Deposition
& Release
3D Models
Annotations
Publications
The Protein Data Bank
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RCSB PDB portal (www.pdb.org)
Using the RCSB PDB website
• Search for entry (by ID, name, keyword, author,
sequence, ligand etc.)
• Browse (by source organism, structure
classification, biological process, function etc.)
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Identify details of a structure
Visualize structures
Download data files for analysis and use
Create reports (tabular, drill down, collage)
Link to various other resources (e.g. PubMed,
UniProt, SCOP, CATH, GO etc.)
Searching
Browsing
Exploring a Structure
Widgets
Visualization Options
• Context-sensitive 3D
Viewers
– Asymmetric unit
– Biological assembly
• Biological assembly
displayed by default
• For X-ray structures:
presumed oligomeric
state displayed
Sequence
Interactive 3D
Views of
Domain Annotations
Exploring Ligand Environments
Poseview
Query Results Browser
Query Refinements
Tabular Reports
Image Collage
MyPDB
• Keep up-to-date with
new structures
• Framework to store
user preferences
• Saves queries in a
private account
• Notifies users via email
when new structures
match stored queries
Resources/Tutorials
• Collection of tutorials:
http://www.rcsb.org/pdb/static.do?p=education_disc
ussion/educational_resources/index.html#tutorials
• Getting started:
http://www.rcsb.org/pdb/static.do?p=general_inform
ation/getting_started/index.html
• Screencasts:
http://www.rcsb.org/pdb/static.do?p=general_inform
ation/screencasts.jsp
• Openhelix tutorial: http://www.openhelix.com/pdb
• Help:
http://www.rcsb.org/pdb/staticHelp.do?p=help/index.
html