This is an important site to take note of when we consider the mutated protein structure. One CA atom (401) is involved in the protein's function and this calcium is bound through interactions with a short loop region (that is rendered in Jmol partly loop, partly helical). The side chains of these catalytic residues are brought close together in the folded protein to form the active site pocket. Cut and past these commands into the console, highlight them and then select run. This is most evident in that there is a new menu item Tools.JSpecView, which opens a new JSpecView frame that includes the current model. We will highlight the catalytic triad to see how residues that are widely spaced in the sequence are brought together in the 3D structure. Jmol 13.0 marks a new collaboration with the JSpecView project with the incorporation of JSpecView into the Jmol application and synchronized communication between the Jmol applet and the JSpecView applet. The catalytic His is residue 254 and the catalytic Asp is 232. We know from the publication associated with 4GW3 ( ) PML contains a hydrolase Ser-His-Asp catalytic triad with the catalytic serine (Ser79) being part of a GXSXG sequence motif. This will render your protein to look like this and spin it round, you can re-orientate the molecule in the Viewer window and then let it spin so you can see different aspects of the protein. As this is a lot of commands to type, open the script Editor window.ĭrag and drop or copy and paste the commands into the Editor window (you may need to use Ctrl+v), and then Run the commands We will use Jmol to highlight these ligands and the two lid helices in the structure. Over 10000000 page views Jmol / JSmol is a molecular viewer for 3D chemical. Ligands in the structure: from the RCSB Summary page we know that 4GW3 has 4 unique ligands. Jmol - An interactive viewer for three-dimensional chemical structures. How does the Pfam sequence domain relate to the 3D fold of the protein?.
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