- 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
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Case study 2: Searching for a ligand
This short tutorial will demonstrate how to find the PDB entries that contain Aspirin, and will show you what information you can extract about this popular drug (from these entries) by using PDBe’s integrated search system.
Task:
1. Go to the PDBe homepage and start typing ‘aspi…’ and the auto-suggest feature will locate where that term occurs in PDB entries.
2. The option under ‘Ligand’ shows details about Aspirin, which has a three-letter code AIN (unique to this molecule in the PDB). You will see a list of entries that contains Aspirin (AIN) (Figure 24).
3. Click on the AIN code under the ‘Ligand’ section to obtain a summary of these entries.
