Yes, you can use Blender to prepare figures for your next paper and the results for sure will look different than the ones obtained with a standard software (hemoglobin [1HBG] as example below)… But given amount of work and really steep learning curve (at least for somebody who tries that for the very first time), I would not recommend Blender that much… 🙂
UPDATE: if you look for a way to import a PDB file into Blender, some instructions are at the bottom of this page.
Freelancing science 