You can generate 3D structure of a protein using prediction software such as I-TASSER, SPARKS-X, or Rosetta. This prediction software can generate an approximate 3D structure from its sequence. To generate 3D structure of a protein with its cysteine residues, you can use the Cysteine Scanner software.

If the protein is in the PDB (Protein Data Bank - https://www.rcsb.org), you can import that file (.pdb) into several different applications.

You can use PyMol, ChimeraX or some other packages. They offer different molecular representations. There are several ways to mark desired structures. You could extract them in different pdb and use different color scheme.

Additionally, if you would like to build bigger structures (or only visualize individual proteins in atomistic representation), you can also use MesoCraft - a rule-based meso-scale modeling application: https://www.nanovis.org/MesoCraft.html

https://www.kaust.edu.sa/docs/kaustlibraries/documents/downloads/kaust-mesocraft.pdf

I hope this helps.

Hi Mahmut. How are you? For 3D protein structure, I recall using Swiss PDB viewer (https://spdbv.unil.ch/disclaim.html#).

Let's keep in touch :)

Have a nice day!

Stef