Open a PDB file when you don’t know the ID

Protein structure files are available for free download via the RCSB Protein Data Bank. If you don’t know the 4-digit PDB ID for a structure, you can locate the structure on the PDB website, and then download it to use later in Protean 3D. Alternatively, you can write down its number and import it using Protean 3D’s File > Open from PDB command, as described here.

1. Go to the Protein Data Bank home page. Locate the search bar near the top of the window.

2. Enter a term (e.g. ‘luciferase,’ ‘feline leukemia,’ etc.).

3. In the ensuing results page, refine the query, if desired.

4. From the list of results, click on a hyperlinked structure name or PDB ID to open the page for that structure.

5. To open the structure in Protean 3D, do either of the following:
   
   

• Make a notation of the PDB ID, then follow these instructions.
  
  
• Download the file to your hard drive and then open it in Protean 3D. To download the file, first locate the Download Files menu in the top right corner of the PDB structure page. Click on the triangle to open the menu, and then choose either PDB File (Text) or PDB File (.gz).

For more information and guides to using PDB, see the topic Useful Links.

*Note: Protean 3D always uses the sequence from the original PDB file. When a PDB file is saved as a .structure file, two copies of the original sequence are stored in that file. The first copy, used whenever the file is opened in Protean 3D, cannot be edited. The second copy can be edited with DNASTAR’s SeqBuilder Pro, and the edits can be viewed in some additional DNASTAR Lasergene applications.