5hdo: Difference between revisions
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The | ==Crystal structure of a nanobody raised against urokinase-type plasminogen activator== | ||
<StructureSection load='5hdo' size='340' side='right'caption='[[5hdo]], [[Resolution|resolution]] 2.16Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5hdo]] is a 4 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=5HDO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HDO 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]] 2.16Å</td></tr> | |||
<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=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=5hdo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hdo OCA], [https://pdbe.org/5hdo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hdo RCSB], [https://www.ebi.ac.uk/pdbsum/5hdo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hdo ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A0F6YEF6_CAMDR A0A0F6YEF6_CAMDR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A peptide segment that binds the active site of a serine protease in a substrate-like manner may behave like an inhibitor or a substrate. However, there is sparse information on which factors determine which behavior a particular peptide segment will exhibit. Here, we describe the first X-ray crystal structure of a nanobody in complex with a serine protease. The nanobody displays a new type of interaction between an antibody and a serine protease as it inserts its CDR-H3 loop into the active site of the protease in a substrate-like manner. The unique binding mechanism causes the nanobody to behave as a strong inhibitor as well as a poor substrate. Intriguingly, its substrate behavior is incomplete, as 30-40% of the nanobody remained intact and inhibitory after prolonged incubation with uPA. Biochemical analysis reveals that an intra-loop interaction network within the CDR-H3 of the nanobody balances its inhibitor versus substrate behavior. Collectively, our results unveil molecular factors, which may be a general mechanism to determine the substrate versus inhibitor behavior of other protease inhibitors. | |||
A Camelid-derived Antibody Fragment Targeting the Active Site of a Serine Protease Balances between Inhibitor and Substrate Behavior.,Kromann-Hansen T, Oldenburg E, Yung KW, Ghassabeh GH, Muyldermans S, Declerck PJ, Huang M, Andreasen PA, Ngo JC J Biol Chem. 2016 May 23. pii: jbc.M116.732503. PMID:27226628<ref>PMID:27226628</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Kromann-Hansen | <div class="pdbe-citations 5hdo" style="background-color:#fffaf0;"></div> | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Camelus dromedarius]] | |||
[[Category: Large Structures]] | |||
[[Category: Kromann-Hansen T]] | |||
Latest revision as of 07:32, 9 August 2023
Crystal structure of a nanobody raised against urokinase-type plasminogen activator
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