2op4: Difference between revisions

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{{Seed}}
[[Image:2op4.png|left|200px]]


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==Crystal Structure of Quorum-Quenching Antibody 1G9==
The line below this paragraph, containing "STRUCTURE_2op4", creates the "Structure Box" on the page.
<StructureSection load='2op4' size='340' side='right'caption='[[2op4]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2op4]] is a 2 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=2OP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OP4 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</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=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
{{STRUCTURE_2op4|  PDB=2op4  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2op4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2op4 OCA], [https://pdbe.org/2op4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2op4 RCSB], [https://www.ebi.ac.uk/pdbsum/2op4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2op4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q5BJZ2_RAT Q5BJZ2_RAT]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/op/2op4_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=2op4 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A large number of Gram-negative bacteria employ N-acyl homoserine lactones (AHLs) as signaling molecules in quorum sensing, which is a population density-dependent mechanism to coordinate gene expression. Antibody RS2-1G9 was elicited against a lactam mimetic of the N-acyl homoserine lactone and represents the only reported monoclonal antibody that recognizes the naturally-occuring N-acyl homoserine lactone with high affinity. Due to its high cross-reactivity, RS2-1G9 showed remarkable inhibition of quorum sensing signaling in Pseudomonas aeruginosa, a common opportunistic pathogen in humans. The crystal structure of Fab RS2-1G9 in complex with a lactam analog revealed complete encapsulation of the polar lactam moiety in the antibody-combining site. This mode of recognition provides an elegant immunological solution for tight binding to an aliphatic, lipid-like ligand with a small head group lacking typical haptenic features, such as aromaticity or charge, which are often incorporated into hapten design to generate high-affinity antibodies. The ability of RS2-1G9 to discriminate between closely related AHLs is conferred by six hydrogen bonds to the ligand. Conversely, cross-reactivity of RS2-1G9 towards the lactone is likely to originate from conservation of these hydrogen bonds as well as an additional hydrogen bond to the oxygen of the lactone ring. A short, narrow tunnel exiting at the protein surface harbors a portion of the acyl chain and would not allow entry of the head group. The crystal structure of the antibody without its cognate lactam or lactone ligands revealed a considerably altered antibody-combining site with a closed binding pocket. Curiously, a completely buried ethylene glycol molecule mimics the lactam ring and, thus, serves as a surrogate ligand. The detailed structural delineation of this quorum-quenching antibody will aid further development of an antibody-based therapy against bacterial pathogens by interference with quorum sensing.


===Crystal Structure of Quorum-Quenching Antibody 1G9===
Crystal structures of a quorum-quenching antibody.,Debler EW, Kaufmann GF, Kirchdoerfer RN, Mee JM, Janda KD, Wilson IA J Mol Biol. 2007 May 18;368(5):1392-402. Epub 2007 Mar 6. PMID:17400249<ref>PMID:17400249</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2op4" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17400249}}, adds the Publication Abstract to the page
*[[Antibody 3D structures|Antibody 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17400249 is the PubMed ID number.
*[[Sandbox 20009|Sandbox 20009]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
{{ABSTRACT_PUBMED_17400249}}
== References ==
 
<references/>
==About this Structure==
__TOC__
2OP4 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OP4 OCA].
</StructureSection>
 
[[Category: Large Structures]]
==Reference==
<ref group="xtra">PMID:17400249</ref><references group="xtra"/>
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Debler, E W.]]
[[Category: Debler EW]]
[[Category: Kirchdoerfer, R N.]]
[[Category: Kirchdoerfer RN]]
[[Category: Wilson, I A.]]
[[Category: Wilson IA]]
[[Category: Antibody]]
[[Category: Fab]]
[[Category: Homoserine lactone]]
[[Category: Immunoglobulin]]
[[Category: Induced fit]]
[[Category: Quorum sensing]]
 
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Retrieved from "https://proteopedia.org/2op4"