Fasta to PDB

I am new comer.I have a fasta sequence of a protein urease A from a South Asian strain but I can't find related PDB file in RCSB or EBI databank. How I can get PDB file of this sequence.I tried the homology modeling in swiss modelling. I want to use the pdb file to be used in Swiss PDB viewer.Also how I can find the active site?

sequence

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updated 4.3 years ago by Ram

• written 11.4 years ago by mbstuanindya •

1 answer

There's no straight-forward answer. If there's no existing crystal structure then you're left with either ab initio prediction or homology prediction. Neither of these are perfect, but there are tools for each if you search for them. Regarding finding the active site, how well that will work will depend entirely on how accurate the prediction turns out to be and what's already known about the class of proteins. If you already know residues involved in its action, then perhaps you can find them clustered together as a pocket on the surface or in a groove. There's really no simple generic solution.

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written 11.4 years ago by Devon Ryan

You can try ab initio prediction at the Robetta online server. However, if your protein is large (>120 residues) you cannot expect to get a valid result. In case of homology modelling, you need to check whether you have templates. A sequence search against the Protein Databank should help you with this.

As Devon said though, this is far more complex than you might think. Identifying valid templates is not always straight-forward. In case you're attempting to use ab initio modelling, it makes it even harder because it's difficult to truly believe the result you might get. I would suggest you do a little reading around the topic before you start!

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updated 4.3 years ago by Ram

• written 11.4 years ago by Felix_Sim