- 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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What is the best representative structure?
Which structure should you pick?
The protein myoglobin from the globin protein family returns multiple hits. Which one should you pick for a starting model for molecular replacement or for ligand docking purposes?
The best representative structure from a particular protein family is always the top hit (PDB entry 5XL0 in this example, Figure 14). This is followed by the remaining entries from the same family in order of model and data quality.
How is the quality of a structure assessed?
The structure quality index (resolution of the structure, model geometry and fit of model to experimental data where experimental data is available) for every entry is represented as a slider graphic bar.
The entries are already sorted based on their structure quality, which is the harmonic average of all the criteria of the validation percentile. The validation percentile reported in the PDB validation report is based on the recommendation of the X-ray validation task force (1).