5vij - Revision history

OCA at 13:49, 4 October 2023

2023-10-04T13:49:28Z

←Older revision		Revision as of 13:49, 4 October 2023
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	<StructureSection load='5vij' size='340' side='right'caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5vij' size='340' side='right'caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Buffalo_rat Buffalo rat~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ddn 5ddn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ddn 5ddn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene>~~</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.105Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vii\|5vii]], [[5vih\|5vih]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Grin1, Nmdar1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]), Grin2a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vij OCA], [https://pdbe.org/5vij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vij RCSB], [https://www.ebi.ac.uk/pdbsum/5vij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vij ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vij OCA], [~~http~~://pdbe.org/5vij PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vij RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vij PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vij ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref> [[http://www.uniprot.org/uniprot/NMDE1_RAT NMDE1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Activation requires binding of agonist to both types of subunits.	+	[https://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Buffalo rat]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Conti, P]]	+	[[Category: Rattus norvegicus]]
-	[[Category: Hansen~~, K B~~]]	+	[[Category: Conti P]]
-	[[Category: Mou, T C]]	+	[[Category: Hansen KB]]
-	[[Category: Pinto, A]]	+	[[Category: Mou T-C]]
-	[[Category: Sprang~~, S R~~]]	+	[[Category: Pinto A]]
-	[[Category: Tamborini, L]]	+	[[Category: Sprang SR]]
-	~~[[Category: Antagonist]]~~	+	[[Category: Tamborini L]]
-	~~[[Category: Nmda receptor]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 09:35, 1 January 2020

2020-01-01T09:35:12Z

←Older revision		Revision as of 09:35, 1 January 2020
Line 1:		Line 1:

	==Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC==		==Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC==
-	<StructureSection load='5vij' size='340' side='right' caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='5vij' size='340' side='right'caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ddn 5ddn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ddn 5ddn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vii\|5vii]], [[5vih\|5vih]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vii\|5vii]], [[5vih\|5vih]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Grin1, Nmdar1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]), Grin2a ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vij OCA], [http://pdbe.org/5vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vij RCSB], [http://www.ebi.ac.uk/pdbsum/5vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vij ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vij OCA], [http://pdbe.org/5vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vij RCSB], [http://www.ebi.ac.uk/pdbsum/5vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vij ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5vij" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vij" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate receptor 3D structures\|Glutamate receptor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Buffalo rat]]
		+	[[Category: Large Structures]]
	[[Category: Conti, P]]		[[Category: Conti, P]]
	[[Category: Hansen, K B]]		[[Category: Hansen, K B]]

OCA at 19:59, 15 November 2017

2017-11-15T19:59:46Z

←Older revision		Revision as of 19:59, 15 November 2017
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5vij" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vij" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ionotropic Glutamate Receptors\|Ionotropic Glutamate Receptors]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:55, 17 August 2017

2017-08-17T05:55:05Z

←Older revision		Revision as of 05:55, 17 August 2017
Line 3:		Line 3:
	<StructureSection load='5vij' size='340' side='right' caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5vij' size='340' side='right' caption='[[5vij]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=5ddn 5ddn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vii\|5vii]], [[5vih\|5vih]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vii\|5vii]], [[5vih\|5vih]]</td></tr>
Line 10:		Line 10:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref> [[http://www.uniprot.org/uniprot/NMDE1_RAT NMDE1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Activation requires binding of agonist to both types of subunits.		[[http://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref> [[http://www.uniprot.org/uniprot/NMDE1_RAT NMDE1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Activation requires binding of agonist to both types of subunits.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	NMDA-type glutamate receptors are ligand-gated ion channels that contribute to excitatory neurotransmission in the central nervous system (CNS). Most NMDA receptors comprise two glycine-binding GluN1 and two glutamate-binding GluN2 subunits (GluN2A-D). We describe highly potent (S)-5-[(R)-2-amino-2-carboxyethyl]-4,5-dihydro-1H-pyrazole-3-carboxylic acid (ACEPC) competitive GluN2 antagonists, of which ST3 has a binding affinity of 52 nM at GluN1/2A and 782 nM at GluN1/2B receptors. This 15-fold preference of ST3 for GluN1/2A over GluN1/2B is improved compared with NVP-AAM077, a widely used GluN2A-selective antagonist, which we show has 11-fold preference for GluN1/2A over GluN1/2B. Crystal structures of the GluN1/2A agonist binding domain (ABD) heterodimer with bound ACEPC antagonists reveal a binding mode in which the ligands occupy a cavity that extends toward the subunit interface between GluN1 and GluN2A ABDs. Mutational analyses show that the GluN2A preference of ST3 is primarily mediated by four nonconserved residues that are not directly contacting the ligand, but positioned within 12 A of the glutamate binding site. Two of these residues influence the cavity occupied by ST3 in a manner that results in favorable binding to GluN2A, but occludes binding to GluN2B. Thus, we reveal opportunities for the design of subunit-selective competitive NMDA receptor antagonists by identifying a cavity for ligand binding in which variations exist between GluN2A and GluN2B subunits. This structural insight suggests that subunit selectivity of glutamate-site antagonists can be mediated by mechanisms in addition to direct contributions of contact residues to binding affinity.
		+
		+	Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits.,Lind GE, Mou TC, Tamborini L, Pomper MG, De Micheli C, Conti P, Pinto A, Hansen KB Proc Natl Acad Sci U S A. 2017 Aug 15;114(33):E6942-E6951. doi:, 10.1073/pnas.1707752114. Epub 2017 Jul 31. PMID:28760974<ref>PMID:28760974</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vij" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ionotropic Glutamate Receptors\|Ionotropic Glutamate Receptors]]
	== References ==		== References ==
	<references/>		<references/>

OCA: Protected "5vij" [edit=sysop:move=sysop]

2017-04-27T14:03:01Z

Protected "5vij" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:03, 27 April 2017

OCA: New page: ==Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC==
2017-04-27T14:02:59Z

New page: ==Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC== <StructureSection load='5vij' size='340' side='right' caption=...

New page

==Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-bromophenyl-ACEPC==
<StructureSection load='5vij' size='340' side='right' caption='[[5vij]], [[Resolution|resolution]] 2.10Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VIJ OCA]. For a guided tour on the structure components use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VIJ FirstGlance]. 
</td></tr><tr id='ligand'><td class="sblockLbl">[[Ligand|Ligands:]]</td><td class="sblockDat"><scene name='pdbligand=5DX:5-[(2R)-2-AMINO-2-CARBOXYETHYL]-1-(4-BROMOPHENYL)-1H-PYRAZOLE-3-CARBOXYLIC+ACID'>5DX</scene>, <scene name='pdbligand=GLY:GLYCINE'>GLY</scene></td></tr>
<tr id='related'><td class="sblockLbl">[[Related_structure|Related:]]</td><td class="sblockDat">[[5vii|5vii]], [[5vih|5vih]]</td></tr>
<tr id='resources'><td class="sblockLbl">Resources:</td><td class="sblockDat">[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5vij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vij OCA], [http://pdbe.org/5vij PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vij RCSB], [http://www.ebi.ac.uk/pdbsum/5vij PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vij ProSAT]</td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/NMDZ1_RAT NMDZ1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Mediated by glycine. Plays a key role in synaptic plasticity, synaptogenesis, excitotoxicity, memory acquisition and learning. It mediates neuronal functions in glutamate neurotransmission. Is involved in the cell surface targeting of NMDA receptors.<ref>PMID:15996549</ref> [[http://www.uniprot.org/uniprot/NMDE1_RAT NMDE1_RAT]] NMDA receptor subtype of glutamate-gated ion channels possesses high calcium permeability and voltage-dependent sensitivity to magnesium. Activation requires binding of agonist to both types of subunits.
== References ==
<references/>
TOC
</StructureSection>
[[Category: Conti, P]]
[[Category: Hansen, K B]]
[[Category: Mou, T C]]
[[Category: Pinto, A]]
[[Category: Sprang, S R]]
[[Category: Tamborini, L]]
[[Category: Antagonist]]
[[Category: Nmda receptor]]
[[Category: Receptor]]
[[Category: Transport protein]]