Hi all,
I have a number of proteins mainly from specific protozoans, Dictyostelium discoideum & humans. I need to find the active sites of each. I've used phyre2 to generate the structures and currently using Pymol to look at the structures.
I've tried using PDB files but unable to locate any, I've looked on unitprot to see the listed active sites and can't find any. I've followed a bunch of YouTube tutorials on how to find them with some wacky results. Online websites for pasting in the fasta file. No luck on any front and I'm completely out of ideas.
I'm towards the end of Mphil write up year, so my knowledge and experience with this is some what lacking.
The rate of mutation of amino acids in the active site is very restricted, or even completely conserved. This can easily be visualised when you align orthologous sequences with a multiple sequence alignment software like ClustalX. To do this you have to use BlastP against the Uniprot or NCBI RefSeq database. First identify a number of orthologs of your protein. Select only the best hits for the alignment so that you 'll be sure that they are all orthologous sequences and align them. If you're lucky you'll be able to immediately identify the conserved regions..
Since you have a PDB file (a good one I suppose), you can go through some servers, such as GASS-WEB, or even PISA. If you know your protein, you can have a hint, such as hydrolases, isomerases, etc.
Other option is to try docking servers, such as SwissDock, Dockthor, etc. Sometimes they suggest a "weird" binding site, but you can get some good insights about your active site.
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