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3qcu

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==Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0)==
==Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0)==
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<StructureSection load='3qcu' size='340' side='right' caption='[[3qcu]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
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<StructureSection load='3qcu' size='340' side='right'caption='[[3qcu]], [[Resolution|resolution]] 1.98&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3qcu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QCU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QCU FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3qcu]] is a 4 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=3QCU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QCU FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NKN:(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL+TETRADECANOATE'>NKN</scene></td></tr>
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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]] 1.979&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qct|3qct]], [[3qcv|3qcv]]</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=NKN:(2R)-2-HYDROXY-3-(PHOSPHONOOXY)PROPYL+TETRADECANOATE'>NKN</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DKFZp686P15220 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), IGKC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=3qcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qcu OCA], [https://pdbe.org/3qcu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qcu RCSB], [https://www.ebi.ac.uk/pdbsum/3qcu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qcu ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3qcu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qcu OCA], [http://pdbe.org/3qcu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qcu RCSB], [http://www.ebi.ac.uk/pdbsum/3qcu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qcu ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q6N089_HUMAN Q6N089_HUMAN]
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Lysophosphatidic acid (LPA) is a common product of glycerophospholipid metabolism and an important mediator of signal transduction. Aberrantly high LPA concentrations accompany multiple disease states. One potential approach for treatment of these diseases, therefore, is the therapeutic application of antibodies that recognize and bind LPA as their antigen. We have determined the X-ray crystal structure of an anti-LPA antibody (LT3015) Fab fragment in its antigen-free form to 2.15 A resolution and in complex with two LPA isotypes (14:0 and 18:2) to resolutions of 1.98 and 2.51 A, respectively. The variable CDR (complementarity-determining region) loops at the antigen binding site adopt nearly identical conformations in the free and antigen-bound crystal structures. The crystallographic models reveal that the LT3015 antibody employs both heavy- and light-chain CDR loops to create a network of eight hydrogen bonds with the glycerophosphate head group of its LPA antigen. The head group is almost completely excluded from contact with solvent, while the hydrocarbon tail is partially solvent-exposed. In general, mutation of amino acid residues at the antigen binding site disrupts LPA binding. However, the introduction of particular mutations chosen strategically on the basis of the structures can positively influence LPA binding affinity. Finally, these structures elucidate the exquisite specificity demonstrated by an anti-lipid antibody for binding a structurally simple and seemingly unconstrained target molecule.
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Biochemical and Structural Characterization of Lysophosphatidic Acid Binding by a Humanized Monoclonal Antibody.,Fleming JK, Wojciak JM, Campbell MA, Huxford T J Mol Biol. 2011 Mar 24. PMID:21392506<ref>PMID:21392506</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 3qcu" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
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*[[3D structures of monoclonal antibody|3D structures of monoclonal antibody]]
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Human]]
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[[Category: Homo sapiens]]
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[[Category: Campbell, M A]]
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[[Category: Large Structures]]
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[[Category: Fleming, J K]]
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[[Category: Campbell M-A]]
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[[Category: Huxford, T]]
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[[Category: Fleming JK]]
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[[Category: Wojciak, J M]]
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[[Category: Huxford T]]
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[[Category: Antibody]]
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[[Category: Wojciak JM]]
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[[Category: Immune system]]
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[[Category: Lysophosphatidic acid binding]]
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Current revision

Crystal structure of the LT3015 antibody Fab fragment in complex with lysophosphatidic acid (14:0)

PDB ID 3qcu

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