03. Getting pdb Files of your Target Protein
3. Getting pdb Files of your Target Protein
3.1 The Protein Data Bank
The Protein Data Bank (PDB) was established as the 1^st^ open access digital data resource in all of biology and medicine. It is today a leading global resource for experimental data central to scientific discovery. Through an internet information portal and downloadable data archive, the PDB provides access to 3D structure data for large biological molecules (proteins, DNA, and RNA).
You can find a crystal structure of your target protein on the PDB website by performing a simple text search. For example, “COVID-19 main protease”, you will find numerous entries via this search function and all records will include information about the source of the crystal structure.
Important features to note are the PDB code (4-digit code, e.g. 6YB7 above), the organism and expression system, details about the authors, and the resolution of the crystal structure. You can download a crystal structure pdb file directly from the website by clicking the “download files” button and selecting pdb format.
3.2 Other Sources
There are other ways to obtain pdb files of your target protein, such as from your supervisor (if they have generated a crystal structure themselves in pdb format) or from the Diamond Light Source website (for COVID-19 projects). The Diamond website has a downloads section under their “for scientists” tab. Here you can download all the crystal structures from their fragment screen, and their high-resolution structure of the main protease (PDB: 6YB7).