3cmp - Revision history

OCA at 12:30, 30 August 2023

2023-08-30T12:30:43Z

← Older revision		Revision as of 12:30, 30 August 2023
Line 3:		Line 3:
	<StructureSection load='3cmp' size='340' side='right'caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3cmp' size='340' side='right'caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cmp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. The January 2016 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cmp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. The January 2016 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</td></tr>
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LCN2, HNL, NGAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [https://pdbe.org/3cmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [https://www.ebi.ac.uk/pdbsum/3cmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmp 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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [https://pdbe.org/3cmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [https://www.ebi.ac.uk/pdbsum/3cmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>		[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 23:		Line 23:
	==See Also==		==See Also==
	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]		*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
	*[[Siderocalin\|Siderocalin]]		*[[Siderocalin 3D structures\|Siderocalin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Human~~]]		[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Siderocalin]]		[[Category: Siderocalin]]
	[[Category: Clifton~~, M C~~]]		[[Category: Clifton MC]]
	[[Category: Strong~~, R K]]~~		[[Category: Strong RK]]
	~~[[Category: Antimicrobial protein]]~~
	~~[[Category: Enterobactin]]~~
	~~[[Category: Glycoprotein]]~~
	~~[[Category: Iron]]~~
	~~[[Category: Lipocalin]]~~
	~~[[Category: Pyrrolidone carboxylic acid]]~~
	~~[[Category: Secreted]]~~
	~~[[Category: Siderophore~~]]

OCA at 19:11, 20 October 2021

2021-10-20T19:11:25Z

← Older revision		Revision as of 19:11, 20 October 2021
Line 1:		Line 1:

	==Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin==		==Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin==
	<StructureSection load='3cmp' size='340' side='right' caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3cmp' size='340' side='right'caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cmp]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Human Human]. The January 2016 RCSB PDB [~~http~~://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [~~http~~://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cmp]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. The January 2016 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CMP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LCN2, HNL, NGAL ([~~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">LCN2, HNL, NGAL ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [~~http~~://pdbe.org/3cmp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3cmp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmp 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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [https://pdbe.org/3cmp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [https://www.ebi.ac.uk/pdbsum/3cmp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>		[[https://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 29:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
			[[Category: Large Structures]]
	[[Category: RCSB PDB Molecule of the Month]]		[[Category: RCSB PDB Molecule of the Month]]
	[[Category: Siderocalin]]		[[Category: Siderocalin]]

OCA at 13:15, 7 November 2018

2018-11-07T13:15:16Z

← Older revision		Revision as of 13:15, 7 November 2018
Line 1:		Line 1:

	==Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin==		==Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin==
	<StructureSection load='3cmp' size='340' side='right' caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3cmp' size='340' side='right' caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LCN2, HNL, NGAL ([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">LCN2, HNL, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://pdbe.org/3cmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp 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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://pdbe.org/3cmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cmp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cmp_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cmp_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 22:		Line 23:
	==See Also==		==See Also==
	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]		*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
			*[[Siderocalin\|Siderocalin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:15, 7 February 2016

2016-02-07T14:15:47Z

← Older revision		Revision as of 14:15, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3cmp' size='340' side='right' caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='3cmp' size='340' side='right' caption='[[3cmp]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cmp]] is a 3 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=3CMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cmp]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. The January 2016 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Siderocalin'' by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2016_1 10.2210/rcsb_pdb/mom_2016_1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LCN2, HNL, NGAL ([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">LCN2, HNL, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp 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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://pdbe.org/3cmp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3cmp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>

Line 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Homo sapiens~~]]		[[Category: Human]]
			[[Category: RCSB PDB Molecule of the Month]]
			[[Category: Siderocalin]]
	[[Category: Clifton, M C]]		[[Category: Clifton, M C]]
	[[Category: Strong, R K]]		[[Category: Strong, R K]]
Line 36:		Line 38:
	[[Category: Pyrrolidone carboxylic acid]]		[[Category: Pyrrolidone carboxylic acid]]
	[[Category: Secreted]]		[[Category: Secreted]]
	~~[[Category: Siderocalin]]~~
	[[Category: Siderophore]]		[[Category: Siderophore]]

OCA at 15:51, 24 December 2014

2014-12-24T15:51:20Z

← Older revision		Revision as of 15:51, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3cmp]] is a 3 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=3CMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMP FirstGlance]. <br>		<table><tr><td colspan='2'>[[3cmp]] is a 3 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=3CMP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CMP FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DBH:2,3-DIHYDROXY-BENZOIC+ACID'>DBH</scene>, <scene name='pdbligand=EB4:N,N,N-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)'>EB4</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LCN2, HNL, NGAL ([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">LCN2, HNL, NGAL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp 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=3cmp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cmp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3cmp RCSB], [http://www.ebi.ac.uk/pdbsum/3cmp PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/NGAL_HUMAN NGAL_HUMAN]] Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5-DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth.<ref>PMID:12453413</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 22:
	==See Also==		==See Also==
	*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]		*[[Neutrophil gelatinase-associated lipocalin\|Neutrophil gelatinase-associated lipocalin]]
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Clifton, M C.]]		[[Category: Clifton, M C]]
	[[Category: Strong, R K.]]		[[Category: Strong, R K]]
	[[Category: Antimicrobial protein]]		[[Category: Antimicrobial protein]]
	[[Category: Enterobactin]]		[[Category: Enterobactin]]

OCA at 20:47, 2 October 2014

2014-10-02T20:47:50Z

@@ Line 1: / Line 1: @@
-[[Image:3cmp.png|left|200px]]
+==Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin==
-{{STRUCTURE_3cmp|  PDB=3cmp  |  SCENE=  }}
+==See Also==
+*[[Neutrophil gelatinase-associated lipocalin|Neutrophil gelatinase-associated lipocalin]]
-===Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin===
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
 [[Category: Clifton, M C.]]

OCA: Protected "3cmp" [edit=sysop:move=sysop]

2013-01-07T21:54:19Z

Protected "3cmp" [edit=sysop:move=sysop]

← Older revision	Revision as of 21:54, 7 January 2013
(No difference)

OCA at 21:54, 7 January 2013

2013-01-07T21:54:14Z

← Older revision		Revision as of 21:54, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~		[[Image:3cmp.png\|left\|200px]]
	[[Image:3cmp.~~jpg~~\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3cmp", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3cmp\| PDB=3cmp \| SCENE= }}		{{STRUCTURE_3cmp\| PDB=3cmp \| SCENE= }}

Line 14:		Line 7:

	==About this Structure==		==About this Structure==
	~~3CMP~~ is a 3 ~~chains~~ structure ~~of sequences~~ 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=3CMP OCA].		[[3cmp]] is a 3 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=3CMP OCA].
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Clifton, M C.]]		[[Category: Clifton, M C.]]
Line 27:		Line 20:
	[[Category: Siderocalin]]		[[Category: Siderocalin]]
	[[Category: Siderophore]]		[[Category: Siderophore]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 13 10:25:13 2009''~~

OCA at 07:25, 13 May 2009

2009-05-13T07:25:17Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+{{Seed}}
-The entry 3cmp is ON HOLD  until Paper Publication
+<!--
-Authors: Clifton, M.C., Strong, R.K.
+===Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin===
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 10 12:31:32 2008''
+==About this Structure==

OCA at 09:31, 10 September 2008

2008-09-10T09:31:32Z

← Older revision		Revision as of 09:31, 10 September 2008
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 3cmp is ON HOLD		The entry 3cmp is ON HOLD until Paper Publication

	Authors: Clifton, M.C., Strong, R.K.		Authors: Clifton, M.C., Strong, R.K.
Line 7:		Line 7:
	Description: Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin		Description: Crystal structure of Siderocalin (NGAL, Lipocalin 2) K125A mutant complexed with Ferric Enterobactin

			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 10 12:31:32 2008''
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 11 09~~:32~~:47~~ 2008''