The protein doesn't have any conserved domains nor any structural part of the protein has been deduced by X-ray crystallography and NMR.
Is it a fusion protein or single protein.
Usually when the number of the amino acid is very high and if you didnt get any template for model, you need to split your protein sequence into 200-300 amino acid bits and do blastp search. Then you will get some template based on the template you can get simple models . From that generate a full length model.
It is not the usual way, but the fusion protein was designed by such way.
Note: it will not give efficient model.
Can you tell the name of protein, i am really interested to know about the protein
It is a single protein.
And splitting the protein would not give better results like you said.
Is there any other way??
You cant find a full length template for this protein. I dont think there will be other way to get the structure. Even crystallization of this big protein is also very difficult. The only way is modeling. If you are really curious about the structure you need to work through splitting the protein and generate model. Just give a try. with the help of these tools you can generate model in an hour.
1. Blastp(sequence alignment)
2. Easymod( Modeling)
3. Fpmod(fusion protein modeling)
4. pymol (to analyse the stucture)
If it doesn't works out means. you can directly mail and discuss it with developers of modeler, swissmodeler etc. They may give you fruitful suggestions.
All the best
hey thanks Mr. Saravananprabhu Nadarajan.
I'll give it a try :) .
You can try I-TASSER server to predict the structure. It is one of the best modelling tools available to predict the structure of proteins without any known homologous structures. But the server can only accept protein sequences with
I've worked in I-TASSER.
But didnt know i could request them personally. Will try it!
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