View source for 5yd4


==Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A)==
<StructureSection load='5yd4' size='340' side='right'caption='[[5yd4]], [[Resolution|resolution]] 1.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5yd4]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YD4 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5yd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yd4 OCA], [https://pdbe.org/5yd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yd4 RCSB], [https://www.ebi.ac.uk/pdbsum/5yd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yd4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/KV2A6_MOUSE KV2A6_MOUSE] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Molecular recognition is a fundamental event at the core of essentially every biological process. In particular, intermolecular H-bonds have been recognized as key stabilizing forces in antibody-antigen interactions resulting in exquisite specificity and high affinity. Although equally abundant, the role of intramolecular H-bonds is far less clear and not universally acknowledged. Herein, we have carried out a molecular-level study to dissect the contribution of intramolecular H-bonds in a flexible peptide for the recognition by an antibody. We show that intramolecular H-bonds may have a profound, multifaceted and favorable effect on the binding affinity by up to 2 kcal mol-1 of free energy. Collectively, our results suggest that antibodies are fine tuned to recognize transiently stabilized structures of flexible peptides in solution, for which intramolecular H-bonds play a key role.

Intramolecular H-bonds govern the recognition of a flexible peptide by an antibody.,Miyanabe K, Akiba H, Kuroda D, Nakakido M, Kusano-Arai O, Iwanari H, Hamakubo T, Caaveiro JMM, Tsumoto K J Biochem. 2018 Jul 1;164(1):65-76. doi: 10.1093/jb/mvy032. PMID:29924367<ref>PMID:29924367</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5yd4" style="background-color:#fffaf0;"></div>

==See Also==
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Caaveiro JMM]]
[[Category: Miyanabe K]]
[[Category: Tsumoto K]]