Hi
I want to make 3D model of PAH enzyme(a tetramer E) to assess some compound heterozygote effects. Do you know any site to let me modify each subunit with mutation of interest?
You have already the pdb of the structure? You may use some bioinformatic softwares (pymol, yasara etc.) to substitute the amino acids, if you are not making a lot of mutations. After that you can just try to optimize and minimize the energy if you really need to, rather than seeing some interactions that will be disrupted.
After making the monomer model that includes mutation, use a docking tool to generate a dimer or tetramer with different mutations. You will need a file for each mutation.
If mutations are in places that do not impact oligomer formation, use a model of WT tetramer and then introduce mutations.
Jorgaq Pata
yes ,thanks
(PDB ID: 6HYC )this is PBD ID for full length protein
Faeze Khaghani since you have the full structure, just use pymol to introduce the mutations, be careful though, if your mutations may disrupt the tetramer, you probably won't see that in the structure. The aim of this would be to check if there are any interactions that will be disrupted or not.
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