Suppose, I want to model a protein's structure (containing total of 350 residues) for which there is no complete experimental structure available. However, I got two different PDB files each contains approximately one half of the protein (e.g. PDB file 1 contains residues 3-150 and PDB file 2 contains residues 200-350). Is there a way, I can use both the file to construct a complete 3D structure of the protein.
N.B.: I have observed such cases for Receptor proteins. As these proteins are usually very long, it is usually not the case that the entire protein is resolved in one single PDB file rather different PDB entries contain different segments of the protein.
Thanks in advance.
Dear Umar Faruq Chowdhury ,
There are several questions/discussions here on RG with some good advices:
https://www.researchgate.net/post/How_do_you_combine_two_pdb_protein_structure_files
https://www.researchgate.net/post/How_do_you_combine_two_pdb_protein_structure_files
The overall message is that there are multiple ways to achieve this (some pretty straightforward). However, the difficult part is: you have no overlapping sections, which leaves you with the problem how to use structural alignment to link the two parts.
You need a homologous template that you can use to link the domains. So, you can use your FASTA form of your protein and “BLAST” to see you if there are proteins that show some degree of resemblance. You can also try I-Tasser (https://zhanglab.ccmb.med.umich.edu/I-TASSER/), this will render you a prediction of the 3D structure of your protein and you can see how your pdb structures fit in and take it from there.
Hope this helps you any further.
Best regards.
PS. I came across the following paper that might be of interest to you: Article Improved protein structure prediction using predicted interr...
Dear Rob Keller, thank you very much for your reply. Highly appreciate the help.
You can use "Modeller" to build a model from multiple templates.
https://salilab.org/modeller/9.25/manual/node21.html
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