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1gyk

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{{Seed}}
 
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[[Image:1gyk.png|left|200px]]
 
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==Serum Amyloid P Component co-crystallised with MOBDG at neutral pH==
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The line below this paragraph, containing "STRUCTURE_1gyk", creates the "Structure Box" on the page.
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<StructureSection load='1gyk' size='340' side='right'caption='[[1gyk]], [[Resolution|resolution]] 2.20&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'>[[1gyk]] is a 5 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=1GYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GYK 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]] 2.2&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CDG:METHYL+4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE'>CDG</scene></td></tr>
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{{STRUCTURE_1gyk| PDB=1gyk | 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=1gyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gyk OCA], [https://pdbe.org/1gyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gyk RCSB], [https://www.ebi.ac.uk/pdbsum/1gyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gyk ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN] Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.
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== Function ==
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[https://www.uniprot.org/uniprot/SAMP_HUMAN SAMP_HUMAN] Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.
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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/gy/1gyk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1gyk 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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Two monoclinic (P2(1)) crystal forms of human serum amyloid P component (SAP) in complex with the 4,6-pyruvate acetal of beta-D-galactose (MObetaDG) were prepared. Structure analysis by molecular replacement and refinement at 2.2A resolution revealed that crystal form 1 (a=95.76A, b=70.53A, c=103.41A, beta=96.80 degrees) contained a pentamer in the asymmetric unit with a structure very similar to that of the published search model. The mode of ligand co-ordination was also similar except that four of the five subunits showed bound ligand with an additional H-bond between O1 of the galactose and the side-chain of Lys79. One sub-unit showed no bound ligand and a vacant calcium site close to a crystal contact. The 2.6A resolution structure of crystal form 2 (a=118.60A, b=109.10A, c=120.80A and beta=95.16 degrees ) showed ten sub-units in the asymmetric unit, all with two bound calcium ions and ligand. The most extensive protein-protein interactions between pentamers describe an AB face-to-face interaction involving 15 ion pairs that sandwiches five molecules of bound MObetaDG at the interface.
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===SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH===
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The structures of crystalline complexes of human serum amyloid P component with its carbohydrate ligand, the cyclic pyruvate acetal of galactose.,Thompson D, Pepys MB, Tickle I, Wood S J Mol Biol. 2002 Jul 26;320(5):1081-6. PMID:12126626<ref>PMID:12126626</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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<div class="pdbe-citations 1gyk" style="background-color:#fffaf0;"></div>
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<!--
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_12126626}}, adds the Publication Abstract to the page
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*[[Serum amyloid P-component|Serum amyloid P-component]]
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(as it appears on PubMed at http://www.pubmed.gov), where 12126626 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_12126626}}
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__TOC__
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</StructureSection>
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==About this Structure==
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1GYK 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=1GYK OCA].
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==Reference==
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The structures of crystalline complexes of human serum amyloid P component with its carbohydrate ligand, the cyclic pyruvate acetal of galactose., Thompson D, Pepys MB, Tickle I, Wood S, J Mol Biol. 2002 Jul 26;320(5):1081-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12126626 12126626]
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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: Pepys, M B.]]
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[[Category: Pepys MB]]
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[[Category: Thompson, D.]]
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[[Category: Thompson D]]
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[[Category: Tickle, I.]]
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[[Category: Tickle I]]
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[[Category: Wood, S P.]]
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[[Category: Wood SP]]
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[[Category: Amyloid lectin]]
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[[Category: Glycoprotein]]
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[[Category: Pentraxin]]
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[[Category: Plasma]]
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[[Category: Polymorphism]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 06:19:21 2008''
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Current revision

Serum Amyloid P Component co-crystallised with MOBDG at neutral pH

PDB ID 1gyk

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