How do you biologists draw a protein when you write a paper?
As mentioned in the comments, diagrams like these are generated by software. The one I use is Chimera, it is free. The structure of the protein is recorded as a list of atoms and their 3D coordinates, as well as bonds, helices, sheets, etc. When a structure file is loaded, the software generates a 3D model based on the data. The user can rotate the model, move it, zoom in, change the color, an many other options, then export a 2D image when they are satisfied. If you want to use structure data files other researchers have generated, the Protein Data Bank is probably the best resource. Research articles that involve new structural data will list the PDB numbers of their structures near the end. In the article you link, the authors include pdb accession numbers for the structures they used for their figures. For the image you use as an example, here is the caption:


  Fig. 56 PEGylation of four solvent-accessible Tyr residues of chymotrypsinogen (pdb: 1EX3) reported by Francis et al.