1pz5

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{{Seed}}
 
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[[Image:1pz5.png|left|200px]]
 
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==Structural basis of peptide-carbohydrate mimicry in an antibody combining site==
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The line below this paragraph, containing "STRUCTURE_1pz5", creates the "Structure Box" on the page.
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<StructureSection load='1pz5' size='340' side='right'caption='[[1pz5]], [[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'>[[1pz5]] is a 3 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=1PZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PZ5 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pz5 OCA], [https://pdbe.org/1pz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pz5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pz5 ProSAT]</span></td></tr>
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{{STRUCTURE_1pz5| PDB=1pz5 | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/A2NHM3_MOUSE A2NHM3_MOUSE]
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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/pz/1pz5_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=1pz5 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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The structure of a complex between the Fab fragment of the antibody (SYA/J6) specific for the cell surface O-antigen polysaccharide of the pathogen Shigella flexneri Y and an octapeptide (Met-Asp-Trp-Asn-Met-His-Ala-Ala), a functional mimic of the O-antigen, has been determined at 1.8-A resolution. Comparison of the structure with that of the complex with the pentasaccharide antigen [--&gt;2)-alpha-L-Rha-(1--&gt;2)-alpha-L-Rha-(1--&gt;3)-alpha-L-Rha-(1--&gt;3)-beta-D- GlcNAc-(1--&gt;2)-alpha-L-Rha-(1--&gt;] reveals the molecular recognition process by which a peptide mimics a carbohydrate in binding to an antibody. The binding modes of the two ligands differ considerably. Octapeptide binding complements the shape of the combining site groove much better than pentasaccharide binding. Moreover, the peptide makes a much greater number of contacts (126), which are mostly van der Waals interactions, with the Fab than the saccharide (74). An unusual feature is also the involvement of 12 water molecules in mediating hydrogen bonds between residues within the peptide or of the peptide and Fab. Despite better shape complementarity and greater number of contacts, the octapeptide binds with an affinity (KA = 2.5 x 10(5) M-1, measured by calorimetry) only approximately 2-fold tighter than the pentasaccharide. The structural results are relevant to the design of peptide mimetics with improved affinity for use as vaccines.
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===Structural basis of peptide-carbohydrate mimicry in an antibody combining site===
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Structural basis of peptide-carbohydrate mimicry in an antibody-combining site.,Vyas NK, Vyas MN, Chervenak MC, Bundle DR, Pinto BM, Quiocho FA Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15023-8. Epub 2003 Nov 25. PMID:14645714<ref>PMID:14645714</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 1pz5" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_14645714}}, adds the Publication Abstract to the page
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*[[Antibody 3D structures|Antibody 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 14645714 is the PubMed ID number.
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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== References ==
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{{ABSTRACT_PUBMED_14645714}}
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<references/>
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__TOC__
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==About this Structure==
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</StructureSection>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PZ5 OCA].
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[[Category: Large Structures]]
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[[Category: Mus musculus]]
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==Reference==
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[[Category: Bundle DR]]
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Structural basis of peptide-carbohydrate mimicry in an antibody-combining site., Vyas NK, Vyas MN, Chervenak MC, Bundle DR, Pinto BM, Quiocho FA, Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15023-8. Epub 2003 Nov 25. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14645714 14645714]
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[[Category: Chervenak MC]]
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[[Category: Bundle, D R.]]
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[[Category: Pinto BM]]
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[[Category: Chervenak, M C.]]
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[[Category: Quiocho FA]]
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[[Category: Pinto, B M.]]
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[[Category: Vyas MN]]
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[[Category: Quiocho, F A.]]
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[[Category: Vyas NK]]
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[[Category: Vyas, M N.]]
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[[Category: Vyas, N K.]]
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[[Category: Antibody-antigen structure]]
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[[Category: Peptide-carbohydrate mimicry]]
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[[Category: Vaccine design]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:10:43 2008''
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Current revision

Structural basis of peptide-carbohydrate mimicry in an antibody combining site

PDB ID 1pz5

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