- Course overview
- Search within this course
- What is PDBe?
- Why do we need PDBe?
- When to use PDBe?
- How to access and navigate PDBe?
- Guided exercise 1: Giardia lamlia
- Exercise 1: How do I search PDB for Giardia lamblia?
- Exercise 1: How many proteins are there in the PDB for Giardia lamblia?
- Exercise 1: How many of these proteins function as enzymes?
- Exercise 1: Which part of the cell do these proteins come from?
- Exercise 1: What type of ligands do they interact with?
- Guided exercise 2: Glycolysis process
- Exercise 2: How do I search the PDB for enzymes involved in glycolysis?
- Exercise 2: Are all the 10 enzyme structures that are involved in the glycolytic pathway present in the PDB?
- Exercise 2: What part of the cell do the enzymes belong to?
- Exercise 2: How do I identify the different classes of enzymes (e.g. hydrolase) that participate in glycolysis?
- Exercise 2: How many of them display nucleotide binding activity?
- Exercise 2: Which protein family/families does the enzyme Glucokinase belong to?
- Exercise 2: How do I identify the best representative structure from each of the protein families?
- Exploring a PDB entry
- Summary
- Test your knowledge
- Your feedback
- Learn more
- Get help and support on PDBe
- References
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.
Useful tips for searching
Here we present a few tips that can help you when conducting searches in PBDe.
- The search /query is stored in the URL. You can just bookmark the page to save this for future use.
- You can choose to select multiple entries from your search, allowing you to download search information for multiple entries at once.
- It is useful to look at the results from different viewpoints:
- I need to know all the entries returned by the query
- ‘Entries’ tab
- What unique macromolecules (i.e. protein/DNA/RNA) are found in these entries?
- ‘Macromolecules’ tab
- What sort of compounds are associated with the entries?
- ‘Compounds’ tab
- What protein families do these entries belong?
- ‘Protein families’ tab
- I need to know all the entries returned by the query
Check out the mini tutorials on Author and Ligand searching to learn more about exploring protein data bank using PDBe search