4h1q - Revision history

OCA at 16:02, 14 March 2024

OCA — Thu, 14 Mar 2024 16:02:00 GMT

←Older revision		Revision as of 16:02, 14 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)-N-(4-{[(3S)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.59Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)-N-(4-{[(3S)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [https://pdbe.org/4h1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [https://www.ebi.ac.uk/pdbsum/4h1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h1q ProSAT]</span></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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [https://pdbe.org/4h1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [https://www.ebi.ac.uk/pdbsum/4h1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h1q ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>		[https://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects.
-
-	Crystallization of bi-functional ligand protein complexes.,Antoni C, Vera L, Devel L, Catalani MP, Czarny B, Cassar-Lajeunesse E, Nuti E, Rossello A, Dive V, Stura EA J Struct Biol. 2013 Apr 6. pii: S1047-8477(13)00086-5. doi:, 10.1016/j.jsb.2013.03.015. PMID:23567804<ref>PMID:23567804</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4h1q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 07:53, 3 November 2022

OCA — Thu, 03 Nov 2022 07:53:17 GMT

←Older revision		Revision as of 07:53, 3 November 2022
Line 1:		Line 1:

	==Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.==		==Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.==
-	<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>	+	<StructureSection load='4h1q' size='340' side='right'caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)-N-(4-{[(3S)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene~~></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)-N-(4-{[(3S)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [https://pdbe.org/4h1q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [https://www.ebi.ac.uk/pdbsum/4h1q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4h1q ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [~~http~~://pdbe.org/4h1q PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4h1q PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4h1q ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] Defects in MMP9 may be a cause of susceptibility to intervertebral disc disease (IDD) [MIM:[~~http~~://omim.org/entry/603932 603932]]; also known as lumbar disk herniation (LDH). IDD is one of the most common musculo-skeletal disorders and the predominant cause of low-back pain and unilateral leg pain.<ref>PMID:18455130</ref> Defects in MMP9 are the cause of metaphyseal anadysplasia type 2 (MANDP2) [MIM:[~~http~~://omim.org/entry/613073 613073]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.	+	[https://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN] Defects in MMP9 may be a cause of susceptibility to intervertebral disc disease (IDD) [MIM:[https://omim.org/entry/603932 603932]; also known as lumbar disk herniation (LDH). IDD is one of the most common musculo-skeletal disorders and the predominant cause of low-back pain and unilateral leg pain.<ref>PMID:18455130</ref> Defects in MMP9 are the cause of metaphyseal anadysplasia type 2 (MANDP2) [MIM:[https://omim.org/entry/613073 613073]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>	+	[https://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:

	==See Also==		==See Also==
-	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]	+	*[[Matrix metalloproteinase 3D structures\|Matrix metalloproteinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Gelatinase B~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Human~~]]	+	[[Category: Large Structures]]
-	[[Category: Cassar-Lajeunesse, E]]	+	[[Category: Cassar-Lajeunesse E]]
-	[[Category: Catalani~~, M P~~]]	+	[[Category: Catalani MP]]
-	[[Category: Dive, V]]	+	[[Category: Dive V]]
-	[[Category: Nuti, E]]	+	[[Category: Nuti E]]
-	[[Category: Rossello, A]]	+	[[Category: Rossello A]]
-	[[Category: Stura~~, E A~~]]	+	[[Category: Stura EA]]
-	[[Category: Vera, L]]	+	[[Category: Vera L]]
-	~~[[Category: Gelatinase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Hydrolase/twin inhibitor]]~~	+
-	~~[[Category: Zincin-like~~]]	+

OCA at 11:52, 7 October 2017

OCA — Sat, 07 Oct 2017 11:52:56 GMT

←Older revision		Revision as of 11:52, 7 October 2017
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(~~BIPHENYL~~-4-~~YLSULFONYL~~)(~~PROPAN~~-2-~~YLOXY~~)~~AMINO~~]-4-(~~HYDROXYAMINO~~)-4-~~OXOBUTYL~~]~~AMINO~~}-4-~~OXOBUTYL~~)-N-(4-{[(3S)-3-[(~~BIPHENYL~~-4-~~YLSULFONYL~~)(~~PROPAN~~-2-~~YLOXY~~)~~AMINO~~]-4-(~~HYDROXYAMINO~~)-4-~~OXOBUTYL~~]~~AMINO~~}-4-~~OXOBUTYL~~)~~BENZENE~~-1,3-~~DICARBOXAMIDE~~'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)-N-(4-{[(3S)-3-[(biphenyl-4-ylsulfonyl)(propan-2-yloxy)amino]-4-(hydroxyamino)-4-oxobutyl]amino}-4-oxobutyl)benzene-1,3-dicarboxamide'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>

OCA at 16:05, 17 May 2017

OCA — Wed, 17 May 2017 16:05:35 GMT

←Older revision		Revision as of 16:05, 17 May 2017
Line 1:		Line 1:
		+
	==Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.==		==Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.==
	<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [http://www.ebi.ac.uk/pdbsum/4h1q PDBsum]</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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [http://pdbe.org/4h1q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [http://www.ebi.ac.uk/pdbsum/4h1q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4h1q ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4h1q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:20, 12 August 2015

OCA — Wed, 12 Aug 2015 08:20:05 GMT

←Older revision		Revision as of 08:20, 12 August 2015
Line 2:		Line 2:
	<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>		<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [http://www.ebi.ac.uk/pdbsum/4h1q PDBsum]</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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [http://www.ebi.ac.uk/pdbsum/4h1q PDBsum]</span></td></tr>
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Gelatinase B]]		[[Category: Gelatinase B]]
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Cassar-Lajeunesse, E]]		[[Category: Cassar-Lajeunesse, E]]
	[[Category: Catalani, M P]]		[[Category: Catalani, M P]]

OCA at 09:56, 20 January 2015

OCA — Tue, 20 Jan 2015 09:56:07 GMT

←Older revision		Revision as of 09:56, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_4h1q\| PDB=4h1q \| SCENE= }}~~	+	==Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.==
-	===Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.===	+	<StructureSection load='4h1q' size='340' side='right' caption='[[4h1q]], [[Resolution\|resolution]] 1.59Å' scene=''>
-	{{~~ABSTRACT_PUBMED_23567804}~~}	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4H1Q FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=0XX:N-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE'>0XX</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ow1\|2ow1]], [[4h3x\|4h3x]], [[4h2e\|4h2e]], [[4h30\|4h30]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CLG4B, MMP9 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Gelatinase_B Gelatinase B], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.35 3.4.24.35] </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=4h1q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4h1q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4h1q RCSB], [http://www.ebi.ac.uk/pdbsum/4h1q PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] Defects in MMP9 may be a cause of susceptibility to intervertebral disc disease (IDD) [MIM:[http://omim.org/entry/603932 603932]]; also known as lumbar disk herniation (LDH). IDD is one of the most common musculo-skeletal disorders and the predominant cause of low-back pain and unilateral leg pain.<ref>PMID:18455130</ref> Defects in MMP9 are the cause of metaphyseal anadysplasia type 2 (MANDP2) [MIM:[http://omim.org/entry/613073 613073]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.		[[http://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] Defects in MMP9 may be a cause of susceptibility to intervertebral disc disease (IDD) [MIM:[http://omim.org/entry/603932 603932]]; also known as lumbar disk herniation (LDH). IDD is one of the most common musculo-skeletal disorders and the predominant cause of low-back pain and unilateral leg pain.<ref>PMID:18455130</ref> Defects in MMP9 are the cause of metaphyseal anadysplasia type 2 (MANDP2) [MIM:[http://omim.org/entry/613073 613073]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Homodimerization is important in signal transduction and can play a crucial role in many other biological systems. To obtaining structural information for the design of molecules able to control the signalization pathways, the proteins involved will have to be crystallized in complex with ligands that induce dimerization. Bi-functional drugs have been generated by linking two ligands together chemically and the relative crystallizability of complexes with mono-functional and bi-functional ligands has been evaluated. There are problems associated with crystallization with such ligands, but overall, the advantages appear to be greater than the drawbacks. The study involves two matrix metalloproteinases, MMP-12 and MMP-9. Using flexible and rigid linkers we show that it is possible to control the crystal packing and that by changing the ligand-enzyme stoichiometric ratio, one can toggle between having one bi-functional ligand binding to two enzymes and having the same ligand bound to each enzyme. The nature of linker and its point of attachment on the ligand can be varied to aid crystallization, and such variations can also provide valuable structural information about the interactions made by the linker with the protein. We report here the crystallization and structure determination of seven ligand-dimerized complexes. These results suggest that the use of bi-functional drugs can be extended beyond the realm of protein dimerization to include all drug design projects.

-	~~==Function==~~	+	Crystallization of bi-functional ligand protein complexes.,Antoni C, Vera L, Devel L, Catalani MP, Czarny B, Cassar-Lajeunesse E, Nuti E, Rossello A, Dive V, Stura EA J Struct Biol. 2013 Apr 6. pii: S1047-8477(13)00086-5. doi:, 10.1016/j.jsb.2013.03.015. PMID:23567804<ref>PMID:23567804</ref>
-	~~[[http~~:~~//www~~.~~uniprot~~.~~org~~/~~uniprot/MMP9_HUMAN MMP9_HUMAN]] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration~~. ~~Could play a role in bone osteoclastic resorption~~. ~~Cleaves KiSS1 at a Gly-\|-Leu bond~~. ~~Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments~~. ~~Degrades fibronectin but not laminin or Pz-peptide~~.<ref>PMID:~~1480034~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4h1q]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Homo_sapiens Homo sapiens]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	<references ~~group="xtra"~~/><~~references~~/>	+	*[[Matrix metalloproteinase\|Matrix metalloproteinase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gelatinase B]]		[[Category: Gelatinase B]]
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Cassar-Lajeunesse, E.]]	+	[[Category: Cassar-Lajeunesse, E]]
-	[[Category: Catalani, M P.]]	+	[[Category: Catalani, M P]]
-	[[Category: Dive, V.]]	+	[[Category: Dive, V]]
-	[[Category: Nuti, E.]]	+	[[Category: Nuti, E]]
-	[[Category: Rossello, A.]]	+	[[Category: Rossello, A]]
-	[[Category: Stura, E A.]]	+	[[Category: Stura, E A]]
-	[[Category: Vera, L.]]	+	[[Category: Vera, L]]
	[[Category: Gelatinase]]		[[Category: Gelatinase]]
	[[Category: Hydrolase-hydrolase inhibitor complex]]		[[Category: Hydrolase-hydrolase inhibitor complex]]
	[[Category: Hydrolase/twin inhibitor]]		[[Category: Hydrolase/twin inhibitor]]
	[[Category: Zincin-like]]		[[Category: Zincin-like]]

OCA at 11:28, 24 April 2013

OCA — Wed, 24 Apr 2013 11:28:40 GMT

←Older revision		Revision as of 11:28, 24 April 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4h1q\| PDB=4h1q \| SCENE= }}
		+	===Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.===
		+	{{ABSTRACT_PUBMED_23567804}}

-	~~The~~ entry ~~4h1q~~ is ~~ON HOLD until Paper Publication~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] Defects in MMP9 may be a cause of susceptibility to intervertebral disc disease (IDD) [MIM:[http://omim.org/entry/603932 603932]]; also known as lumbar disk herniation (LDH). IDD is one of the most common musculo-skeletal disorders and the predominant cause of low-back pain and unilateral leg pain.<ref>PMID:18455130</ref> Defects in MMP9 are the cause of metaphyseal anadysplasia type 2 (MANDP2) [MIM:[http://omim.org/entry/613073 613073]]. Metaphyseal anadysplasia consists of an abnormal bone development characterized by severe skeletal changes that, in contrast with the progressive course of most other skeletal dysplasias, resolve spontaneously with age. Clinical characteristics are evident from the first months of life and include slight shortness of stature and a mild varus deformity of the legs. Patients attain a normal stature in adolescence and show improvement or complete resolution of varus deformity of the legs and rhizomelic micromelia.

-	~~Authors~~: ~~Stura, E~~.A.~~, Vera, L~~.~~, Cassar~~-~~Lajeunesse, E~~.~~, Nuti, E., Catalani, M.P., Dive,~~ V.~~, Rossello, A~~.	+	==Function==
		+	[[http://www.uniprot.org/uniprot/MMP9_HUMAN MMP9_HUMAN]] May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-\|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide.<ref>PMID:1480034</ref>

-	~~Description: Crystal~~ structure ~~of mutant MMP~~-~~9 catalytic domain in~~ complex ~~with a~~ twin inhibitor.	+	==About this Structure==
		+	[[4h1q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4H1Q OCA].
		+
		+	==Reference==
		+	<references group="xtra"/><references/>
		+	[[Category: Gelatinase B]]
		+	[[Category: Homo sapiens]]
		+	[[Category: Cassar-Lajeunesse, E.]]
		+	[[Category: Catalani, M P.]]
		+	[[Category: Dive, V.]]
		+	[[Category: Nuti, E.]]
		+	[[Category: Rossello, A.]]
		+	[[Category: Stura, E A.]]
		+	[[Category: Vera, L.]]
		+	[[Category: Gelatinase]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Hydrolase/twin inhibitor]]
		+	[[Category: Zincin-like]]

OCA at 06:13, 14 November 2012

OCA — Wed, 14 Nov 2012 06:13:28 GMT

←Older revision		Revision as of 06:13, 14 November 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4h1q is ON HOLD	+	The entry 4h1q is ON HOLD until Paper Publication

	Authors: Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., Dive, V., Rossello, A.		Authors: Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., Dive, V., Rossello, A.

	Description: Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.		Description: Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.

OCA: Protected "4h1q" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2012 06:57:45 GMT

Protected "4h1q" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:57, 19 September 2012

OCA: New page: '''Unreleased structure''' The entry 4h1q is ON HOLD Authors: Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., Dive, V., Rossello, A. Description: Crystal struct...

OCA — Wed, 19 Sep 2012 06:57:44 GMT

New page: '''Unreleased structure''' The entry 4h1q is ON HOLD Authors: Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., Dive, V., Rossello, A. Description: Crystal struct...

New page

'''Unreleased structure'''

The entry 4h1q is ON HOLD

Authors: Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Nuti, E., Catalani, M.P., Dive, V., Rossello, A.

Description: Crystal structure of mutant MMP-9 catalytic domain in complex with a twin inhibitor.