1od9: Difference between revisions

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-[[Image:1od9.jpg|left|200px]]
- {{Structure
+==N-terminal of Sialoadhesin in complex with Me-a-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ compound)==
-|PDB= 1od9 |SIZE=350|CAPTION= <scene name='initialview01'>1od9</scene>, resolution 2.10&Aring;
+<StructureSection load='1od9' size='340' side='right'caption='[[1od9]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-|SITE= <scene name='pdbsite=BND:So4+Binding+Site+For+Chain+A'>BND</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene> and <scene name='pdbligand=BND:ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC'>BND</scene>
+<table><tr><td colspan='2'>[[1od9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OD9 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BND:ME-A-N-BENZOYL-AMINO-9-DEOXY-NEU5AC'>BND</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=1od9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1od9 OCA], [https://pdbe.org/1od9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1od9 RCSB], [https://www.ebi.ac.uk/pdbsum/1od9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1od9 ProSAT]</span></td></tr>
+</table>
-'''N-TERMINAL OF SIALOADHESIN IN COMPLEX WITH ME-A-9-N-BENZOYL-AMINO-9-DEOXY-NEU5AC (BENZ COMPOUND)'''
+== Function ==
+[https://www.uniprot.org/uniprot/SN_MOUSE SN_MOUSE] Acts as an endocytic receptor mediating clathrin dependent endocytosis. Macrophage-restricted adhesion molecule that mediates sialic-acid dependent binding to lymphocytes, including granulocytes, monocytes, natural killer cells, B-cells and CD8 T-cells (By similarity). Preferentially binds to alpha-2,3-linked sialic acid. Binds to SPN/CD43 on T-cells. May play a role in hematopoiesis. May act as a counter-receptor for CLEC10A in lymph node.<ref>PMID:15364954</ref>
+== Evolutionary Conservation ==
-==Overview==
+[[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/od/1od9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1od9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
 The Siglec family of receptors mediates cell surface interactions through recognition of sialylated glycoconjugates. The crystal structure of the N-terminal immunoglobulin-like domain of the Siglec sialoadhesin (SnD1) in complex with 2,3-sialyllactose has informed the design of sialic acid analogs (sialosides) that bind Siglecs with significantly enhanced affinities and specificities. Binding assays against sialoadhesin (Sn; Siglec-1), CD22 (Siglec-2), and MAG (Siglec-4) show a 10- to 300-fold reduction in IC(50) values (relative to methyl-alpha-Neu5Ac) for three sialosides bearing aromatic group modifications of the glycerol side chain: Me-alpha-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ), Me-alpha-9-N-(naphthyl-2-carbonyl)-amino-9-deoxy-Neu5Ac (NAP), and Me-alpha-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP). Crystal structures of these sialosides in complex with SnD1 suggest explanations for the differences in specificity and affinity, providing further ideas for compound design of physiological and potentially therapeutic relevance.
-==About this Structure==
+Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin.,Zaccai NR, Maenaka K, Maenaka T, Crocker PR, Brossmer R, Kelm S, Jones EY Structure. 2003 May;11(5):557-67. PMID:12737821<ref>PMID:12737821</ref>
-OD9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OD9 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure-guided design of sialic acid-based Siglec inhibitors and crystallographic analysis in complex with sialoadhesin., Zaccai NR, Maenaka K, Maenaka T, Crocker PR, Brossmer R, Kelm S, Jones EY, Structure. 2003 May;11(5):557-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12737821 12737821]
+</div>
+<div class="pdbe-citations 1od9" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Brossmer R]]
-[[Category: Brossmer, R.]]
+[[Category: Crocker PR]]
-[[Category: Crocker, P R.]]
+[[Category: Jones EY]]
-[[Category: Jones, E Y.]]
+[[Category: Kelm S]]
-[[Category: Kelm, S.]]
+[[Category: Maenaka K]]
-[[Category: Maenaka, K.]]
+[[Category: Maenaka T]]
-[[Category: Maenaka, T.]]
+[[Category: Zaccai NR]]
-[[Category: Zaccai, N R.]]
-[[Category: BND]]
-[[Category: SO4]]
-[[Category: carbohydrate binding]]
-[[Category: immune system]]
-[[Category: immunoglobulin superfamily]]
-[[Category: inhibitor design]]
-[[Category: siglec]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:09:12 2008''