I have a sequence (query sequence below) which is composed of some signal peptide, linkers and two identical domains.
The domain has the known structure in PDB, R/S/T chain in 1xu1 (a complex with protein APRIL)
and A chain in 1xut (unbound form).
I like to dock the predicted structure of sequence back to protein APRIL in 1xu1.
How can I predict the structure of such sequence?
P.S.
For better docking later, Using only 1xu1:R as template in structure prediction phase
might be better than using both 1xu1:R and 1xut:A?
Any idea/hint will be appreciated.
The query sequence:
MSGLGRSRRGGRSRVDQEERWSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLRGSSGLGRSRRGGRSRVDQEERWSLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLRSPVNLPPELRRQRSGEVENNSDNSGRYQGLEHRGSEASPALPGLKLSADQVALVYST
The domain sequence:
SLSCRKEQGKFYDHLLRDCISCASICGQHPKQCAYFCENKLR