User:Alice Harmon/Sandbox 2: Difference between revisions

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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.

|'''Left scene''' - The crystal structure [[3ku2]] shows the '''inactive conformation''' of the kinase that is bound only to 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. Note the long α-helices of the CAD and that it is bound across 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.

|'''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 (wireframe and CPK coloring). As in the left scene, the catalytic domain is blue and the CAD is gold. In the model in these default scenes the large lobe of the kinase domain is in approximately the same orientation. When bound to four calcium ions, one in each of the four EF-hands, CAD interacts with the side of the kinase domain that is opposite side from 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. Apo CAD helices</scene> <scene name='55/559103/Kd_critical/5'>3. Inactive kinase domain critical structures</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/5'>1. Default scene</scene> <scene name='55/559103/Holo-ikinase_cad_rainbow/2'>2. Apo CAD</scene> shown in rainbow colors starting with blue at the N-terminal end to red at the C-terminal ends of the domain. <scene name='55/559103/Holo-ikinase_cad_rainbow/3'>3. Apo CAD helices</scene> <scene name='55/559103/Kd_critical/5'>4. Inactive kinase domain critical structures</scene>: ATP binding loop in lime; Subdomain III in orchid; catalytic loop in blue; Mg2+ loop/activation loop in gold.

| <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='~~<scene name='55/559103/Akd_critical/5'>3. Active kinase domain critical structures</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/2'>1. Default Scene</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. Calcium-bound CAD</scene> <scene name='55/559103/Holo-akinase_cad_rainbow/2'>3. CAD bent helices</scene> <scene name='55/559103/Akd_critical/5'>4. Active kinase domain critical structures</scene> in the same color scheme as in the left scene.

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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.
+|'''Left scene''' - The crystal structure [[3ku2]] shows the '''inactive conformation''' of the kinase that is bound only to 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. Note the long α-helices of the CAD and that it is bound across 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.
+|'''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 (wireframe and CPK coloring). As in the left scene, the catalytic domain is blue and the CAD is gold. In the model in these default scenes the large lobe of the kinase domain is in approximately the same orientation. When bound to four calcium ions, one in each of the four EF-hands, CAD interacts with the side of the kinase domain that is opposite side from 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. Apo CAD helices</scene><br><scene name='55/559103/Kd_critical/5'>3. Inactive kinase domain critical structures</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/5'>1. Default scene</scene><Br><scene name='55/559103/Holo-ikinase_cad_rainbow/2'>2. Apo CAD</scene> shown in rainbow colors starting with blue at the N-terminal end to red at the C-terminal ends of the domain. <br><scene name='55/559103/Holo-ikinase_cad_rainbow/3'>3. Apo CAD helices</scene><br><scene name='55/559103/Kd_critical/5'>4. Inactive kinase domain critical structures</scene>: ATP binding loop in lime; Subdomain III in orchid; catalytic loop in blue; Mg2+ loop/activation loop in gold.
-| <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='<scene name='55/559103/Akd_critical/5'>3. Active kinase domain critical structures</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/2'>1. Default Scene</scene><Br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>2. Calcium-bound CAD</scene><br><scene name='55/559103/Holo-akinase_cad_rainbow/2'>3. CAD bent helices</scene><br><scene name='55/559103/Akd_critical/5'>4. Active kinase domain critical structures</scene> in the same color scheme as in the left scene.
 |}