Online tutorial
PDBe
Exploring a Protein Data Bank entry
Time to complete:
1 hour
Written by:
- Sanchayita Sen
- Genevieve Laura Evans
- Deepti Gupta
Last reviewed:
March 2024
All materials are free cultural works licensed under a Creative Commons Attribution 4.0 International (CC BY 4.0) license, except where further licensing details are provided.
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This course will show you how to explore the structural information in a PDB entry using PDBe - EMBL-EBI's resource for the collection, organisation and dissemination of data on biological macromolecular structures.
Who is this course for?
This courses is suitable for anyone interested in learning about PDBe, however undergraduate knowledge of a life science subject would be an advantage. This course follows on from PDBe: Searching the Protein Data Bank.
What will I achieve?
By the end of the course you will be able to:
- Navigate and extract the information from a particular PDB entry using the PDBe
- Download data in an appropriate format
What resources do I need?
There are no specific resources required to complete this course.
DOI:
10.6019/TOL.PDBe-exp-t.2015.00001.1
Course contents
- What information does a PDB entry contain?
- How is the information structured?
- PDB entry overview
- Citation page
- Function and Biology
- Is the protein an enzyme?
- What specific biological processes are associated with the proteins?
- Which sequence family does the protein belong to?
- What protein signatures can be found in the structure?
- What are the structural folds/domains present in the proteins from this entry?
- The SCOP classification of protein folds
- Structure analysis
- Detailed structure analysis
- How can I interactively explore the protein and DNA molecules present in the entry?
- Which amino acids from the protein chain participate in binding interactions with ligands?
- What is the build quality of the protein chain?
- What are the signature domains/folds – Pfam
- What are the signature domains/folds – CATH
- What are the signature domains/folds – SCOP
- What are the probable quaternary structures and biological assemblies?
- Unravelling the symmetry of a virus capsid using assembly information
- Ligands and Environments
- Downloading data from a PDB entry page
- Summary
- Your feedback
- Learn more
- Get help and support on PDBe
How and when to access the course
All our courses are designed with flexibility in mind. You can access them for free at any time, just click on the "Enter Course" button.
It is up to you how you use the course; you can either study the full course or you can focus on sections that are relevant to you. To jump between sections, use the navigation bar on the left or the arrows at the bottom of the page. You can also choose whether to complete the course in one go, or over several visits.
The average time to read through the main body of the course is 3 hours (not including exercises and external links). The time may vary depending on your prior knowledge and how you choose to work through the course.
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Learning something new takes time and practice. We encourage you to:
- Use the activities and quizzes to help you check your learning, recall and apply key concepts. Look out for these icons
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Activities
Quizzes
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