Introduction to the protein data bank
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Introduction to the Protein Data Bank. Learning to Use the RCSB PDB Portal. What is the PDB?. Archive of experimentally determined (X-ray crystallography, NMR, electron microscopy) 3D structural data It contains Coordinates of all atoms in the structure

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Introduction to the protein data bank

Introduction to the Protein Data Bank

Learning to Use the RCSB PDB Portal


What is the pdb
What is the PDB?

  • Archive of experimentally determined (X-ray 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
Why bother with the PDB?

  • 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
The Data Pipeline

Isolation,

Expression,

Purification,

Crystallization

Genomic

Based Target

Selection

Data

Collection

Structure

Determination

PDB Deposition

& Release

3D Models

Annotations

Publications


The protein data bank

1

2

3

4

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2

3

4

The Protein Data Bank


Rcsb pdb portal www pdb org
RCSB PDB portal (www.pdb.org)


Using the rcsb pdb website
Using the RCSB PDB website

  • Searchfor entry (by ID, name, keyword, author, sequence, ligand etc.)

  • Browse(by source organism, structure classification, biological process, function etc.)

  • Identify details of a structure

  • Visualizestructures

  • Downloaddata files for analysis and use

  • Create reports(tabular, drill down, collage)

  • Linkto various other resources (e.g. PubMed, UniProt, SCOP, CATH, GO etc.)






Introduction to the protein data bank

Visualization Options

  • Context-sensitive 3D Viewers

    • Asymmetric unit

    • Biological assembly

  • Biological assembly displayed by default

  • For X-ray structures: presumed oligomeric state displayed


Sequence
Sequence

Interactive 3D

Views of

Domain Annotations


Exploring ligand environments

Poseview

Exploring Ligand Environments






Mypdb
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
Resources/Tutorials

  • Collection of tutorials: http://www.rcsb.org/pdb/static.do?p=education_discussion/educational_resources/index.html#tutorials

  • Getting started:http://www.rcsb.org/pdb/static.do?p=general_information/getting_started/index.html

  • Screencasts: http://www.rcsb.org/pdb/static.do?p=general_information/screencasts.jsp

  • Openhelix tutorial: http://www.openhelix.com/pdb

  • Help: http://www.rcsb.org/pdb/staticHelp.do?p=help/index.html