My protein (AKT2 - 480 residues) possesses 4 domains, PH domain (Residues 1-107), Linker (Residues 108-148), PK domain (Residues 149-408) and C-terminal extension (Residues 409-480).
I have the sequence of the full protein and I also have the crystal structures of the PH domain, PK domain and C-terminal extension but I don't have any information about the structure of the Linker domain (Residues 108-148) and as a result I would like to find a prediction for the Linker structure.
I would like to ask you if it is better to submit only the sequence of the Linker domain in order to have a better prediction for the Linker structure or the full sequence with the known crystal structures of the other domains?
Thank you very much.