Identical structure in different domains.

Question

[Shahzad]

Dear fellows

I have 8 sequences of proteins based on their functional similarity reported by experimental works. Alignment shows very low identity and similarity in these seq. I want to find out is there any binding site which is same in all these proteins and have the capability to bind with same molecule specifically with water molecule. What I need to know is

• from where should I take 3D models of these proteins (any recommended database)
• how to find the binding sites in these proteins.
• how to superimpose or process these model to get the desired binding site having binding capability for water.

---(Databases and tools necessary to do this task)

Further suggestions will be highly appreciated.

Thank you.

Answer 1

[zorbax]

Hi:

ITASSER could help you. It's a "server for protein 3D structure prediction". This server also predicts binding sites.

About the superimpose, well, PyMOL can be helpful with 'align' option in terminal: 'align struc1, struct2'...