User:Anat Levit/Sandbox 1: Difference between revisions

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The TM cavity of PKR1 and PKR2 is quite a narrow cleft, similar to the epinephrine binding site of β2-Adrenergic receptor. It is a narrow and deep cleft that is largely concealed from solvent, which may enable ligand interaction with both walls (via van der Waals contacts). Based on the comparison to 2RH1, we can see that the residues lining the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_based_residues/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.

The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/4' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.

The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/5' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.

Revision as of 21:46, 7 October 2009 view source Anat Levit (talk \| contribs) 77 edits No edit summary ← Older edit		Revision as of 22:07, 7 October 2009 view source Anat Levit (talk \| contribs) 77 edits No edit summary Newer edit →
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	The TM cavity of PKR1 and PKR2 is quite a narrow cleft, similar to the epinephrine binding site of β2-Adrenergic receptor. It is a narrow and deep cleft that is largely concealed from solvent, which may enable ligand interaction with both walls (via van der Waals contacts). Based on the comparison to 2RH1, we can see that the residues lining the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_based_residues/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.		The TM cavity of PKR1 and PKR2 is quite a narrow cleft, similar to the epinephrine binding site of β2-Adrenergic receptor. It is a narrow and deep cleft that is largely concealed from solvent, which may enable ligand interaction with both walls (via van der Waals contacts). Based on the comparison to 2RH1, we can see that the residues lining the <scene name='User:Anat_Levit/Sandbox_1/Pkr1_2rh1_based_residues/3'>PROKR1</scene> binding site are hydrophobic, which may contribute to potential affinity and polar, which can allow for strong directional constraints through electrostatic interactions.
	The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/4' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.		The <scene name='User:Anat_Levit/Sandbox_1/Pkr2_2rh1_residues/5' target='PROKR2'>PROKR2</scene> predicted binding site is almost identical to the PROKR1 site, except for an addition of Ala322 in PROKR2, which is not present in PROKR1, and Glu240 in PROKR1, which is not present in PROKR2.