User:Alice Harmon/Sandbox 2: Difference between revisions

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Crystal structures of inactive and active conformations of CDPK1 from ''Toxoplasma gondii'' show the dramatic conformation change that occurs upon the binding of calcium to the regulatory domain <ref> PMID:20436473 </ref>. See [[Eukaryotic Protein Kinase Catalytic Domain]] for a guide to their structure.

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|'''Left scene''' - The crystal structure [[3ku2]] shows the '''inactive conformation''' of the kinase that is bound only to the ANP (wireframe and CPK coloring). As above, the catalytic domain is blue and the CAD is gold. The large lobe of the kinase domain is in approximately the same orientation as in the left scene. Note the large conformational change in the CAD (long alpha helices) and that it is now bound to the same side of the kinase as the catalytic cleft (marked by the bound ANP), blocking it from binding peptide substrate.

|'''Right scene''' - The crystal structure [[3hx4]] shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding.

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| <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /> '''3ku2 scenes''' <scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene>shown in rainbow colors from the N-terminal (blue) to the C-terminal (red) ends of the domain. <scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. CAD helices</scene> <scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene>

| <applet load='3HX4' size='400' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '55/559103/Holo-akinase/2' /> '''3hx4 scenes''' <scene name='55/559103/Holo-akinase_cad_rainbow/1'>1. Calcium-bound CAD</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. CAD bent helices</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/3'>3. dummy</scene>

| <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /> '''3ku2 scenes''' <scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene> <scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. CAD helices</scene> <scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene>

|-

|The crystal structure [[3hx4]] in the left scene shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding.

|The crystal structure [[3ku2]] in the right scene shows the '''inactive conformation''' of the kinase that is bound only to the ANP (wireframe and CPK coloring). As above, the catalytic domain is blue and the CAD is gold. The large lobe of the kinase domain is in approximately the same orientation as in the left scene. Note the large conformational change in the CAD (long alpha helices) and that it is now bound to the same side of the kinase as the catalytic cleft (marked by the bound ANP), blocking it from binding peptide substrate.

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 Crystal structures of inactive and active conformations of CDPK1 from ''Toxoplasma gondii'' show the dramatic conformation change that occurs upon the binding of calcium to the regulatory domain <ref> PMID:20436473 </ref>. See [[Eukaryotic Protein Kinase Catalytic Domain]] for a guide to their structure.
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+|'''Left scene''' - The crystal structure [[3ku2]] shows the '''inactive conformation''' of the kinase that is bound only to the ANP (wireframe and CPK coloring). As above, the catalytic domain is blue and the CAD is gold. The large lobe of the kinase domain is in approximately the same orientation as in the left scene. Note the large conformational change in the CAD (long alpha helices) and that it is now bound to the same side of the kinase as the catalytic cleft (marked by the bound ANP), blocking it from binding peptide substrate.
+|'''Right scene''' - The crystal structure [[3hx4]] shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding.
+|-
+| <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /><br>'''3ku2 scenes''' <Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene>shown in rainbow colors from the N-terminal (blue) to the C-terminal (red) ends of the domain. <br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. CAD helices</scene><br><scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene>
 | <applet load='3HX4' size='400' frame='true' align='left' caption='3hx4 - active TgCDPK1' scene = '55/559103/Holo-akinase/2' /><Br>'''3hx4 scenes'''<Br><scene name='55/559103/Holo-akinase_cad_rainbow/1'>1. Calcium-bound CAD</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. CAD bent helices</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/3'>3. dummy</scene>
-| <applet load='3ku2' size='400' frame='true' align='left' caption='3ku2 - inactive TgCDPK1' scene = '55/559103/Holo-ikinase/5' /><br>'''3ku2 scenes''' <Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>1. Apo CAD</scene><br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>2. CAD helices</scene><br><scene name='55/559103/Holo-ikinase_cad_rainbow/4'>3. dummy</scene>
-|-
-|The crystal structure [[3hx4]] in the left scene shows the '''active conformation''' of the kinase that is bound to calcium (green spheres) and the ATP analog ANP (also called AMPPNP; shown in wireframe and CPK coloring). The catalytic domain is blue and the calcium activation domain (CAD) is gold. In the kinase domain, ANP sits in the catalytic cleft between the large and small lobes of the domain. CAD is bound to the side of the kinase opposite to the catalytic cleft, making it available for peptide substrate binding.
-|The crystal structure [[3ku2]] in the right scene shows the '''inactive conformation''' of the kinase that is bound only to the ANP (wireframe and CPK coloring). As above, the catalytic domain is blue and the CAD is gold. The large lobe of the kinase domain is in approximately the same orientation as in the left scene. Note the large conformational change in the CAD (long alpha helices) and that it is now bound to the same side of the kinase as the catalytic cleft (marked by the bound ANP), blocking it from binding peptide substrate.
 |}