6jb9: Difference between revisions
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<StructureSection load='6jb9' size='340' side='right'caption='[[6jb9]], [[Resolution|resolution]] 1.15Å' scene=''> | <StructureSection load='6jb9' size='340' side='right'caption='[[6jb9]], [[Resolution|resolution]] 1.15Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[6jb9]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[6jb9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Camelus_dromedarius Camelus dromedarius]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JB9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JB9 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.15Å</td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <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=6jb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jb9 OCA], [https://pdbe.org/6jb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jb9 RCSB], [https://www.ebi.ac.uk/pdbsum/6jb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jb9 ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</div> | </div> | ||
<div class="pdbe-citations 6jb9" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 6jb9" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Antibody 3D structures|Antibody 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Camelus dromedarius]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Akiba | [[Category: Akiba H]] | ||
[[Category: Caaveiro | [[Category: Caaveiro JMM]] | ||
[[Category: Tamura | [[Category: Tamura H]] | ||
[[Category: Tsumoto | [[Category: Tsumoto K]] | ||
Latest revision as of 13:05, 22 November 2023
Crystal structure of nanobody D3-L11 (unbound form)Crystal structure of nanobody D3-L11 (unbound form)
Structural highlights
Publication Abstract from PubMedSingle-domain antibodies (VHHs or nanobodies), developed from heavy chain-only antibodies of camelids, are gaining attention as next-generation therapeutic agents. Despite their small size, the high affinity and specificity displayed by VHHs for antigen molecules rival those of IgGs. How such small antibodies achieve that level of performance? Structural studies have revealed that VHHs tend to recognize concave surfaces of their antigens with high shape-complementarity. However, the energetic contribution of individual residues located at the binding interface has not been addressed in detail, obscuring the actual mechanism by which VHHs target the concave surfaces of proteins. Herein, we show that a VHH specific for hen egg lysozyme, D3-L11, not only displayed the characteristic binding of VHHs to a concave region of the surface of the antigen, but also exhibited a distribution of energetic hot-spots like those of IgGs and conventional protein-protein complexes. The highly preorganized and energetically compact interface of D3-L11 recognizes the concave epitope with high shape complementarity by the classical lock-and-key mechanism. Our results shed light on the fundamental basis by which a particular VHH accommodate to the concave surface of an antigens with high affinity in a specific manner, enriching the mechanistic landscape of VHHs. Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.,Akiba H, Tamura H, Kiyoshi M, Yanaka S, Sugase K, Caaveiro JMM, Tsumoto K Sci Rep. 2019 Oct 29;9(1):15481. doi: 10.1038/s41598-019-50722-y. PMID:31664051[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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