Sandbox Reserved 1649: Difference between revisions

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'''Ligand binding domain (LBD)'''

LBD is constituted of two domains S1 (located juste upstream M1 transmembrane domain) and S2 and has affinity for <scene name='86/868182/Lbd/3'>glutamate</scene> or sometimes [https://en.wikipedia.org/wiki/Glycine Glycine]. Positive charge of amino-group of the agonist binds to negative charges residue of the pocket D731. In [https://proteopedia.org/wiki/index.php/Glutamate_receptor_%28GluA2%29 GlurR], negative charge amino acid is a E731 and is able to form salt bridge with agonist. In NR2A D731 (which corresponds to <scene name='86/868182/D213/3'>D213</scene>) is not able to do salt bridge with amino group because [https://fr.wikipedia.org/wiki/Acide_aspartique aspartate] is one methylene lacking to do it. Amino group of agonist is stabilized by water mediated hydrogen bonds to amino acid Y761 (which corresponds to <scene name='86/868182/Y243/2'>Y243</scene>) and E413 (which correspond to <scene name='86/868182/E14/3'>E14</scene>).<scene name='86/868182/Y243_et_e14/2'>Click here if you want to see E14 and Y243 together</scene>. The high affinity for glutamate agonist may be because of Van der Walls contact between γ-carboxylate group of glutamate and Y730 of S2 domain which is conserved in NR2 protein.<ref name="LBD">DOI 10.1038/nature04089</ref> Amino-group of glutamate also interacts with <scene name='86/868182/T114/3'>T114</scene> and <scene name='86/868182/S112/2'>S112</scene>. <scene name='86/868182/T114_et_s112/2'>(T114 and S112 together).</scene>

LBD is constituted of two domains S1 (located juste upstream M1 transmembrane domain) and S2 and has affinity for <scene name='86/868182/Lbd/3'>glutamate</scene> or sometimes [https://en.wikipedia.org/wiki/Glycine Glycine]. Positive charge of amino-group of the agonist binds to negative charges residue of the pocket D731. In [https://proteopedia.org/wiki/index.php/Glutamate_receptor_%28GluA2%29 GlurR], negative charge amino acid is a E731 and is able to form [https://en.wikipedia.org/wiki/Salt_bridge salt bridge] with agonist. In NR2A D731 (which corresponds to <scene name='86/868182/D213/3'>D213</scene>) is not able to do salt bridge with amino group because [https://fr.wikipedia.org/wiki/Acide_aspartique aspartate] is one methylene lacking to do it. Amino group of agonist is stabilized by water mediated hydrogen bonds to amino acid Y761 (which corresponds to <scene name='86/868182/Y243/2'>Y243</scene>) and E413 (which correspond to <scene name='86/868182/E14/3'>E14</scene>).<scene name='86/868182/Y243_et_e14/2'>Click here if you want to see E14 and Y243 together</scene>. The high affinity for glutamate agonist may be because of Van der Walls contact between γ-carboxylate group of glutamate and Y730 of S2 domain which is conserved in NR2 protein.<ref name="LBD">DOI 10.1038/nature04089</ref> Amino-group of glutamate also interacts with <scene name='86/868182/T114/3'>T114</scene> and <scene name='86/868182/S112/2'>S112</scene>. <scene name='86/868182/T114_et_s112/2'>(T114 and S112 together).</scene>

On the other hand, <scene name='86/868182/Interact_with_nr1/1'>certain amino acids</scene> from this domain interact with NR1 (see NR1/NR2A complex part).

Sandbox Reserved 1649: Difference between revisions

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@@ Line 23: / Line 23: @@
 '''Ligand binding domain (LBD)'''
-LBD is constituted of two domains S1 (located juste upstream M1 transmembrane domain) and S2 and has affinity for <scene name='86/868182/Lbd/3'>glutamate</scene> or sometimes [https://en.wikipedia.org/wiki/Glycine Glycine]. Positive charge of amino-group of the agonist binds to negative charges residue of the pocket D731. In [https://proteopedia.org/wiki/index.php/Glutamate_receptor_%28GluA2%29 GlurR], negative charge amino acid is a E731 and is able to form salt bridge with agonist. In NR2A D731 (which corresponds to <scene name='86/868182/D213/3'>D213</scene>) is not able to do salt bridge with amino group because [https://fr.wikipedia.org/wiki/Acide_aspartique aspartate] is one methylene lacking to do it. Amino group of agonist is stabilized by water mediated hydrogen bonds to amino acid Y761 (which corresponds to <scene name='86/868182/Y243/2'>Y243</scene>) and E413 (which correspond to <scene name='86/868182/E14/3'>E14</scene>).<scene name='86/868182/Y243_et_e14/2'>Click here if you want to see E14 and Y243 together</scene>. The high affinity for glutamate agonist may be because of Van der Walls contact between γ-carboxylate group of glutamate and Y730 of S2 domain which is conserved in NR2 protein.<ref name="LBD">DOI 10.1038/nature04089</ref> Amino-group of glutamate also interacts with <scene name='86/868182/T114/3'>T114</scene> and <scene name='86/868182/S112/2'>S112</scene>. <scene name='86/868182/T114_et_s112/2'>(T114 and S112 together).</scene>
+LBD is constituted of two domains S1 (located juste upstream M1 transmembrane domain) and S2 and has affinity for <scene name='86/868182/Lbd/3'>glutamate</scene> or sometimes [https://en.wikipedia.org/wiki/Glycine Glycine]. Positive charge of amino-group of the agonist binds to negative charges residue of the pocket D731. In [https://proteopedia.org/wiki/index.php/Glutamate_receptor_%28GluA2%29 GlurR], negative charge amino acid is a E731 and is able to form [https://en.wikipedia.org/wiki/Salt_bridge salt bridge] with agonist. In NR2A D731 (which corresponds to <scene name='86/868182/D213/3'>D213</scene>) is not able to do salt bridge with amino group because [https://fr.wikipedia.org/wiki/Acide_aspartique aspartate] is one methylene lacking to do it. Amino group of agonist is stabilized by water mediated hydrogen bonds to amino acid Y761 (which corresponds to <scene name='86/868182/Y243/2'>Y243</scene>) and E413 (which correspond to <scene name='86/868182/E14/3'>E14</scene>).<scene name='86/868182/Y243_et_e14/2'>Click here if you want to see E14 and Y243 together</scene>. The high affinity for glutamate agonist may be because of Van der Walls contact between γ-carboxylate group of glutamate and Y730 of S2 domain which is conserved in NR2 protein.<ref name="LBD">DOI 10.1038/nature04089</ref> Amino-group of glutamate also interacts with <scene name='86/868182/T114/3'>T114</scene> and <scene name='86/868182/S112/2'>S112</scene>. <scene name='86/868182/T114_et_s112/2'>(T114 and S112 together).</scene>
 On the other hand, <scene name='86/868182/Interact_with_nr1/1'>certain amino acids</scene> from this domain interact with NR1 (see NR1/NR2A complex part).