So, it is recommended to study the articles and compare the available structures to find your favorite structure for further analysis. This is a difficult example since there are so many high resolution structures available.
In our case, we could opt for the structures 1DKX and 4EZX.
For many PDB structures, there is also a re-done structure available with a vast amount of information on the quality of the X-ray structure and suggested ‘better’ models e.g. Furthermore, the PDB database has pre-calculated a validation report for all of the structures.Īs an example, have a look at under the section ‘Experiments and Validation’. Usually, the recommended selection criteria are using an X-ray structure with low resolution and low $R_$ factor. Which structures (give the 4-character PDB ID) of the C-terminal domain of DnaK should preferentially be use for analysis and why? solution Solution Question Guidelines which PDB structures to select Click on Structure in the left-side menu and then look at the 3D structure databases table.Click on the accession code (column Entry) to view the protein page of this DnaK from the model organism Escherichia coli.An entry with accession code P0A6Y8 and entry name DNAK_ECOLI should be near the top of this list. The UniProt search engine returns a list of DnaK protein sequences from a variety of organisms.Go to the UniProt website and search for the DnaK protein.Figure 1: Search box hands_on Explore a PDB structure on the Uniprot web site Below is an image of the UniProt search box where you can start your search for proteins. Our first model protein will be the molecular chaperone DnaK from E. In the last cases I recommend to start from the UniProt website at, which is the best annotated protein database in the world. But mostly you have the protein name or you just have a sequence. You might already have the PDB ID (a unique identifier), that’s an easy one. The way of searching for a specific protein structure depends on the data you already have.
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