- 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 1: Searching for structures from a particular author
Task: Find structures from ‘Rossman MG’.
1. Go to the PDBe homepage and start typing ‘Rossmann’ into the search box. You will notice the autocomplete functionality makes some suggested search terms, which appear under different headings.
2. Click on ‘Rossman MG’ under the ‘Author’ heading (highlighted in Figure 20).
3. You will be presented with a list of results (Figure 21). As of January 2024, we have 358 entries with a name ‘Rossmann MG’ in an author list. This can be narrowed down by adding another criterion (see next page).
