User:Alice Harmon/Sandbox 1: Difference between revisions
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To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[1j3h]]. | To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[1j3h]]. | ||
<Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA, open and inactive' scene='55/555705/Apopka/2' /><scene name='55/555705/Twistedlobes/2'>Open, inactive conformation</scene> | <Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA, open and inactive' scene='55/555705/Apopka/2' /> In the right frame: <scene name='55/555705/Twistedlobes/2'>1. Open, inactive conformation</scene><br><scene name='55/555705/Apo_spines/1'>2. Disassembled spines</scene> <Structure load='1atp' size='350' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /><br>In the left frame: <scene name='55/555705/Closedlobes/4'>1. Closed, active conformation</scene><br><scene name='55/555705/Both_spines/2'>2. Assembled catalytic and regulatory spines</scene> | ||
In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop. Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the open conformation they are too far away from each other to interact. | In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop. Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the open conformation they are too far away from each other to interact. | ||