- 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: Sorting your search results
You can sort the results based on different criteria using the pull-down menu (‘sort by’) at the top right-hand side of the search results (Figure 27).
In this case, we have chosen to sort by resolution in descending order – the PDB entry that has the highest resolution will be at the top of the results.
In the panel of every entry (highlighted in yellow), we can see useful information about these entries such as:
- the proteins to which AIN (aspirin) is bound
- the organism from which they were obtained
- the experimental methods used to determine the structures
- the journals where these structures have been published
- which other ligands are present in these entries and many more
- the 3D visualisation of the structure (including AIN and other ligands)
We can next refine our search based on these different criteria.