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1ukm

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[[Image:1ukm.gif|left|200px]]
 
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{{Structure
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==Crystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)==
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|PDB= 1ukm |SIZE=350|CAPTION= <scene name='initialview01'>1ukm</scene>, resolution 1.90&Aring;
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<StructureSection load='1ukm' size='340' side='right'caption='[[1ukm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
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<table><tr><td colspan='2'>[[1ukm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Echis_multisquamatus Echis multisquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKM FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.9&#8491;</td></tr>
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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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}}
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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=1ukm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ukm OCA], [https://pdbe.org/1ukm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ukm RCSB], [https://www.ebi.ac.uk/pdbsum/1ukm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ukm ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)'''
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== Function ==
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[https://www.uniprot.org/uniprot/SLA_ECHML SLA_ECHML] EMS16 is a potent and selective inhibitor of alpha-2/beta-1 (ITGA2/ITGB1) integrin and acts as a potent antagonist of platelet aggregation and cell migration. Binds specifically to the I domain of the alpha-2 subunit, in a metal ion-independent fashion.
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== Evolutionary Conservation ==
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==Overview==
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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/uk/1ukm_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=1ukm 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 ==
Snake venoms contain a number of hemostatically active C-type lectin-like proteins (CLPs), which affect the blood coagulation system, endothelial cells, and platelets. CLPs have broad similarities in structure and possess distinct biological functions. EMS16, a CLP from Echis multisquamatus venom, which is a potent and selective inhibitor of the collagen receptor, glycoprotein Ia/IIa (integrin alpha2beta1), has been used in the present study to examine structure-function relationships in venom CLPs by X-ray crystallography. The structure of EMS16, determined at a resolution of 1.9 A, revealed a heterodimer involved with domain swapping of the central loop as observed in the structures of other CLPs. A part of the glycan was observed and identified as N-acetyl-D-glucosamine (GlcNAc) in the electron density map at Asn21 of subunit B, an expected glycosylation site. EMS16 had a unique, positively charged electrostatic potential patch on the concave surface that may qualify as a site for interaction with the I-domain of the glycoprotein Ia/IIa.
Snake venoms contain a number of hemostatically active C-type lectin-like proteins (CLPs), which affect the blood coagulation system, endothelial cells, and platelets. CLPs have broad similarities in structure and possess distinct biological functions. EMS16, a CLP from Echis multisquamatus venom, which is a potent and selective inhibitor of the collagen receptor, glycoprotein Ia/IIa (integrin alpha2beta1), has been used in the present study to examine structure-function relationships in venom CLPs by X-ray crystallography. The structure of EMS16, determined at a resolution of 1.9 A, revealed a heterodimer involved with domain swapping of the central loop as observed in the structures of other CLPs. A part of the glycan was observed and identified as N-acetyl-D-glucosamine (GlcNAc) in the electron density map at Asn21 of subunit B, an expected glycosylation site. EMS16 had a unique, positively charged electrostatic potential patch on the concave surface that may qualify as a site for interaction with the I-domain of the glycoprotein Ia/IIa.
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==About this Structure==
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Structural characterization of EMS16, an antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus.,Horii K, Okuda D, Morita T, Mizuno H Biochemistry. 2003 Nov 4;42(43):12497-502. PMID:14580195<ref>PMID:14580195</ref>
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1UKM is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Echis_multisquamatus Echis multisquamatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKM OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structural characterization of EMS16, an antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus., Horii K, Okuda D, Morita T, Mizuno H, Biochemistry. 2003 Nov 4;42(43):12497-502. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14580195 14580195]
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</div>
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<div class="pdbe-citations 1ukm" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Echis multisquamatus]]
[[Category: Echis multisquamatus]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Horii, K.]]
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[[Category: Horii K]]
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[[Category: Mizuno, H.]]
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[[Category: Mizuno H]]
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[[Category: Morita, T.]]
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[[Category: Morita T]]
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[[Category: Okuda, D.]]
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[[Category: Okuda D]]
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[[Category: CL]]
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[[Category: GOL]]
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[[Category: NAG]]
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[[Category: c-type lectin]]
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[[Category: domain swapping]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:33:13 2008''
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Current revision

Crystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)

PDB ID 1ukm

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