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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

Function of your protein

PYCR1 is a protein involved in proline biosynthesis. THFA is a ligand that can bind to the active site on the PYCR1 protein. This inhibits PYCR1's ability to bind to proline-5-carboxylate to synthesize proline. Here is a view with the protein at 50% transparency and the ligands colored .

Biological relevance and broader implications

PYRC1 is the target for potential cancer therapy. THFA binds to the active site on the protein and inhibits it's ability to synthesize proline from proline-5-carboxylate. Cancer cells require more proline than a regular human cell, so finding a ligand to bind to the active site of PYCR1 and inhibit the synthesis of proline could potentially work to stop cancer cells growth and division. Unfortunately, THFA is not as good of an inhibitor than other ligands mentioned in the article, so further research is needed to find a better inhibitor.

Important amino acids

Here is a view, with all of the ligands visible. This is a picture of one of the THFA ligands on the PYCR1 protein. THFA interacts with the amino acids Serine 233, Valine 231, Threonine 238, and Alanine 237 from the PYCR1 protein. highlights all of those amino acids in magenta, with the protein transparency set to 90%.

Structural highlights

There are 5 domains. Among all of them, there is about 50% alpha helices, 40% beta sheets, and about 10% other structures. Alpha helices, beta sheets, and some of the other structures all are bonded to the different ligands. Some of the ligands bond to H2O “outside of the loop”. Here is a view of the highlighted in green, and this is a view of the highlighted in pink. This is a view of domain E's . This is a view of 6XOZ.

Other important features

shows us the hydrophobic areas in the protein in comparison with the polar areas. Looking , we can see that the ligands are located in hydrophobic areas. Proline is hydrophobic, meaning in order to bind, the binding site would need to be located in a hydrophobic region on the protein. In this , you can see the locations of all the prolines. In , you can see the hydrophobic areas in grey, polar in pink, and proline in blue. This shows that prolines are located in the hydrophobic areas.

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.