11:8:11 PYMOL NOTES - 1 Subunit of the Monomer R-state...

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1 Subunit of the Monomer R-state
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Interface between dimers. What is the difference between the subunits in the R and T state?
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R-state Is it distance different the yellow atoms on the same subunit or between subunits T-state distances
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R-state distance
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4 Subunits where the dimers interact (R-state)
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T-state bridge In the R-state these 4 residues are clustered. In the T-state the 4 residues are more spaced apart Relative to whether or not if the active site is open or not
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R-state just residues. These residues are very clustered together. This binds substrate very well T-state just residues – 3 residues are clumped together while the other one is far away. This does NOT bind substrates very well.
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Is the dimer interface changing? Yes Where do the allosteric effectors bind? Where is the active site? What residues change between the T and R state? This is R state and binds ADP. And you can tell because of the ring and the orange spheres are phosphorus. Each phosphorus is bound to 4 oxygens
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Know the difference between ADP and PEP.
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11:8:11 PYMOL NOTES - 1 Subunit of the Monomer R-state...

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