2rid

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{{Seed}}
 
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[[Image:2rid.png|left|200px]]
 
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==Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with Allyl 7-O-carbamoyl-L-glycero-D-manno-heptopyranoside==
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The line below this paragraph, containing "STRUCTURE_2rid", creates the "Structure Box" on the page.
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<StructureSection load='2rid' size='340' side='right'caption='[[2rid]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2rid]] 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=2RID OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RID FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=291:PROP-2-EN-1-YL+7-O-CARBAMOYL-L-GLYCERO-ALPHA-D-MANNO-HEPTOPYRANOSIDE'>291</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
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{{STRUCTURE_2rid| PDB=2rid | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rid FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rid OCA], [https://pdbe.org/2rid PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rid RCSB], [https://www.ebi.ac.uk/pdbsum/2rid PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rid ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/2rid_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2rid ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Lipopolysaccharides (LPS) of Gram-negative bacteria are important mediators of bacterial virulence that can elicit potent endotoxic effects. Surfactant protein D (SP-D) shows specific interactions with LPS, both in vitro and in vivo. These interactions involve binding of the carbohydrate recognition domain (CRD) to LPS oligosaccharides (OS); however, little is known about the mechanisms of LPS recognition. Recombinant neck+CRDs (NCRDs) provide an opportunity to directly correlate binding interactions with a crystallographic analysis of the binding mechanism. In these studies, we examined the interactions of wild-type and mutant trimeric NCRDs with rough LPS (R-LPS). Although rat NCRDs bound more efficiently than human NCRDs to Escherichia coli J-5 LPS, both proteins exhibited efficient binding to solid-phase Rd2-LPS and to Rd2-LPS aggregates presented in the solution phase. Involvement of residues flanking calcium at the sugar binding site was demonstrated by reciprocal exchange of lysine and arginine at position 343 of rat and human CRDs. The lectin activity of hNCRDs was inhibited by specific heptoses, including l-glycero-alpha-d-manno-heptose (l,d-heptose), but not by 3-deoxy-alpha-d-manno-oct-2-ulosonic acid (Kdo). Crystallographic analysis of the hNCRD demonstrated a novel binding orientation for l,d-heptose, involving the hydroxyl groups of the side chain. Similar binding was observed for a synthetic alpha1--&gt;3-linked heptose disaccharide corresponding to heptoses I and II of the inner core region in many LPS. 7-O-Carbamoyl-l,d-heptose and d-glycero-alpha-d-manno-heptose were bound via ring hydroxyl groups. Interactions with the side chain of inner core heptoses provide a potential mechanism for the recognition of diverse types of LPS by SP-D.
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===Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with Allyl 7-O-carbamoyl-L-glycero-D-manno-heptopyranoside===
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Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d.,Wang H, Head J, Kosma P, Brade H, Muller-Loennies S, Sheikh S, McDonald B, Smith K, Cafarella T, Seaton B, Crouch E Biochemistry. 2008 Jan 15;47(2):710-20. Epub 2007 Dec 20. PMID:18092821<ref>PMID:18092821</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18092821}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2rid" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18092821 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18092821}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2RID is a [[Single protein]] structure of 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=2RID OCA].
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==Reference==
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Recognition of heptoses and the inner core of bacterial lipopolysaccharides by surfactant protein d., Wang H, Head J, Kosma P, Brade H, Muller-Loennies S, Sheikh S, McDonald B, Smith K, Cafarella T, Seaton B, Crouch E, Biochemistry. 2008 Jan 15;47(2):710-20. Epub 2007 Dec 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18092821 18092821]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Cafarella, T.]]
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[[Category: Cafarella T]]
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[[Category: Crouch, E.]]
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[[Category: Crouch E]]
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[[Category: Head, J.]]
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[[Category: Head J]]
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[[Category: Kosma, P.]]
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[[Category: Kosma P]]
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[[Category: McDonald, B.]]
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[[Category: McDonald B]]
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[[Category: Seaton, B.]]
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[[Category: Seaton B]]
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[[Category: Sheikh, S.]]
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[[Category: Sheikh S]]
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[[Category: Smith, K.]]
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[[Category: Smith K]]
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[[Category: Wang, H.]]
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[[Category: Wang H]]
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[[Category: Carbohydrate recognition]]
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[[Category: Domain trimeric]]
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[[Category: Sugar binding protein]]
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[[Category: Surfactant protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 11:47:33 2008''
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Current revision

Crystal structure of the trimeric neck and carbohydrate recognition domain of human surfactant protein D in complex with Allyl 7-O-carbamoyl-L-glycero-D-manno-heptopyranoside

PDB ID 2rid

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