3ikq - Revision history

OCA at 15:59, 1 November 2023

2023-11-01T15:59:52Z

←Older revision		Revision as of 15:59, 1 November 2023
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	<StructureSection load='3ikq' size='340' side='right'caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3ikq' size='340' side='right'caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ikq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ikq]] is a 3 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=3IKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.25Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SFTPD, PSPD, SFTP4 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [https://pdbe.org/3ikq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [https://www.ebi.ac.uk/pdbsum/3ikq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikq 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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [https://pdbe.org/3ikq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [https://www.ebi.ac.uk/pdbsum/3ikq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.	+	[https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Greenhough~~, T J~~]]	+	[[Category: Greenhough TJ]]
-	[[Category: Shrive~~, A K]]~~	+	[[Category: Shrive AK]]
-	~~[[Category: Collagen]]~~	+
-	~~[[Category: Disulfide bond]]~~	+
-	~~[[Category: Extracellular matrix]]~~	+
-	~~[[Category: Gaseous exchange]]~~	+
-	~~[[Category: Glycoprotein]]~~	+
-	~~[[Category: Hydroxylation]]~~	+
-	~~[[Category: Lectin]]~~	+
-	~~[[Category: Neck+crd]]~~	+
-	~~[[Category: Secreted]]~~	+
-	~~[[Category: Sugar binding protein]]~~	+
-	~~[[Category: Surface film]]~~	+
-	~~[[Category: Trimeric recombinant fragment~~]]	+

OCA at 07:47, 10 November 2021

2021-11-10T07:47:32Z

←Older revision		Revision as of 07:47, 10 November 2021
Line 1:		Line 1:

	==Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D==		==Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D==
-	<StructureSection load='3ikq' size='340' side='right' caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>	+	<StructureSection load='3ikq' size='340' side='right'caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ikq]] is a 3 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=3IKQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3IKQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ikq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IKQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IKQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([~~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">SFTPD, PSPD, SFTP4 ([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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [~~http~~://pdbe.org/3ikq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ikq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikq 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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [https://pdbe.org/3ikq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [https://www.ebi.ac.uk/pdbsum/3ikq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.	+	[[https://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Greenhough, T J]]		[[Category: Greenhough, T J]]
	[[Category: Shrive, A K]]		[[Category: Shrive, A K]]

OCA at 09:21, 19 December 2018

2018-12-19T09:21:32Z

←Older revision		Revision as of 09:21, 19 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D==		==Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D==
	<StructureSection load='3ikq' size='340' side='right' caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='3ikq' size='340' side='right' caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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">SFTPD, PSPD, SFTP4 ([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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://pdbe.org/3ikq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq 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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://pdbe.org/3ikq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ikq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikq_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikq_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>

OCA at 10:14, 7 February 2016

2016-02-07T10:14:11Z

←Older revision		Revision as of 10:14, 7 February 2016
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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">SFTPD, PSPD, SFTP4 ([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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq 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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://pdbe.org/3ikq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3ikq ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3ikq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:19, 24 December 2014

2014-12-24T14:19:58Z

←Older revision		Revision as of 14:19, 24 December 2014
Line 8:		Line 8:
	<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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq 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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 16:18, 21 December 2014

2014-12-21T16:18:58Z

←Older revision		Revision as of 16:18, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3ikq\| PDB=3ikq \| SCENE= }}~~	+	==Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D==
-	===Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D===	+	<StructureSection load='3ikq' size='340' side='right' caption='[[3ikq]], [[Resolution\|resolution]] 2.25Å' scene=''>
-	~~{{ABSTRACT_PUBMED_19799916}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ikq]] is a 3 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=3IKQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3IKQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1pw9\|1pw9]], [[1pwb\|1pwb]], [[3ikp\|3ikp]], [[3ikn\|3ikn]], [[3ikr\|3ikr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SFTPD, PSPD, SFTP4 ([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=3ikq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ikq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ikq RCSB], [http://www.ebi.ac.uk/pdbsum/3ikq PDBsum]</span></td></tr>
		+	</table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ik/3ikq_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</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].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of human lung surfactant protein D with a series of bound ligands have been determined. While the structures reveal various different binding modes, all utilise a similarly positioned pair of mannose-type O3' and O4' hydroxyls with no direct interaction between any non-terminal sugar and protein. The orientation, position, and interactions of the bound terminal sugar depend on the sugar itself, the presence and form of glycosidic linkage, and the environment in the crystal, which, via Asp325, places stereochemical and electronic constraints, different for the three different subunits in the homotrimer, on the ligand-binding site. As a direct consequence of this influence, the other binding-pocket flanking residue, Arg343, exhibits variable conformation and variable interactions with bound ligand and leaves open to question which orientation of terminal mannobiose, and of other terminal disaccharides, may be present in extended physiological ligands. The combined structural evidence shows that there is significant flexibility in recognition; that Asp325, in addition to Arg343, is an important determinant of ligand selectivity, recognition, and binding; and that differences in crystal contact interfaces exert, through Asp325, significant influence on preferred binding modes.

-	~~==Function==~~	+	Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325.,Shrive AK, Martin C, Burns I, Paterson JM, Martin JD, Townsend JP, Waters P, Clark HW, Kishore U, Reid KB, Greenhough TJ J Mol Biol. 2009 Dec 11;394(4):776-88. Epub 2009 Sep 30. PMID:19799916<ref>PMID:19799916</ref>
-	~~[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover~~ of ~~pulmonary~~ surfactant. ~~Binds strongly maltose residues and to a lesser extent other alpha~~-~~glucosyl moieties~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3ikq]] is~~ a ~~3 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=3IKQ OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:019799916</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Greenhough, T J.]]	+	[[Category: Greenhough, T J]]
-	[[Category: Shrive, A K.]]	+	[[Category: Shrive, A K]]
	[[Category: Collagen]]		[[Category: Collagen]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]

OCA at 14:21, 19 February 2014

2014-02-19T14:21:09Z

←Older revision		Revision as of 14:21, 19 February 2014
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	===Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D===		===Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D===
	{{ABSTRACT_PUBMED_19799916}}		{{ABSTRACT_PUBMED_19799916}}
		+
		+	==Function==
		+	[[http://www.uniprot.org/uniprot/SFTPD_HUMAN SFTPD_HUMAN]] Contributes to the lung's defense against inhaled microorganisms. May participate in the extracellular reorganization or turnover of pulmonary surfactant. Binds strongly maltose residues and to a lesser extent other alpha-glucosyl moieties.

	==About this Structure==		==About this Structure==
-	[[3ikq]] 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=3IKQ OCA].	+	[[3ikq]] is a 3 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=3IKQ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:019799916</ref><~~ref~~ group="xtra"~~>PMID:012888356<~~/~~ref~~><references ~~group="xtra"~~/>	+	<ref group="xtra">PMID:019799916</ref><references group="xtra"/><references/>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Greenhough, T J.]]		[[Category: Greenhough, T J.]]
	[[Category: Shrive, A K.]]		[[Category: Shrive, A K.]]

OCA at 10:44, 13 March 2013

2013-03-13T10:44:28Z

←Older revision		Revision as of 10:44, 13 March 2013
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-	[[Image:3ikq.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ikq", 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_3ikq\| PDB=3ikq \| SCENE= }}		{{STRUCTURE_3ikq\| PDB=3ikq \| SCENE= }}
-
	===Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D===		===Crystal structure of alpha 1-2 mannobiose bound trimeric human lung surfactant protein D===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19799916}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19799916 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19799916}}		{{ABSTRACT_PUBMED_19799916}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19799916~~</ref><ref group="xtra">PMID:~~12888356~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019799916</ref><ref group="xtra">PMID:012888356</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Greenhough, T J.]]		[[Category: Greenhough, T J.]]
	[[Category: Shrive, A K.]]		[[Category: Shrive, A K.]]
-	[[Category: Calcium]]
-	[[Category: Coiled coil]]
	[[Category: Collagen]]		[[Category: Collagen]]
	[[Category: Disulfide bond]]		[[Category: Disulfide bond]]
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	[[Category: Lectin]]		[[Category: Lectin]]
	[[Category: Neck+crd]]		[[Category: Neck+crd]]
-	[[Category: Polymorphism]]
	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
	[[Category: Surface film]]		[[Category: Surface film]]
	[[Category: Trimeric recombinant fragment]]		[[Category: Trimeric recombinant fragment]]

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

2011-03-14T12:47:26Z

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

←Older revision

Revision as of 12:47, 14 March 2011

OCA at 12:47, 14 March 2011

2011-03-14T12:47:25Z

←Older revision		Revision as of 12:47, 14 March 2011
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-	{{Seed}}
	[[Image:3ikq.png\|left\|200px]]		[[Image:3ikq.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~3IKQ~~ is a 3 ~~chains~~ structure with ~~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=3IKQ OCA].	+	[[3ikq]] 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=3IKQ OCA].

	==Reference==		==Reference==
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	[[Category: Surface film]]		[[Category: Surface film]]
	[[Category: Trimeric recombinant fragment]]		[[Category: Trimeric recombinant fragment]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 28 14:33:49 2010''