2rdk: Difference between revisions

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


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==Five site mutated Cyanovirin-N with Mannose dimer bound==
The line below this paragraph, containing "STRUCTURE_2rdk", creates the "Structure Box" on the page.
<StructureSection load='2rdk' size='340' side='right'caption='[[2rdk]], [[Resolution|resolution]] 1.35&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'>[[2rdk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Nostoc_ellipsosporum Nostoc ellipsosporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RDK 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]] 1.35&#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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PRD_900111:2alpha-alpha-mannobiose'>PRD_900111</scene></td></tr>
{{STRUCTURE_2rdk|  PDB=2rdk  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2rdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rdk OCA], [https://pdbe.org/2rdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rdk RCSB], [https://www.ebi.ac.uk/pdbsum/2rdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rdk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CVN_NOSEL CVN_NOSEL] Mannose-binding lectin.<ref>PMID:9210678</ref> <ref>PMID:12678493</ref>
== 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/rd/2rdk_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=2rdk ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Cyanovirin (CV-N) is a small lectin with potent HIV neutralization activity, which could be exploited for a mucosal defense against HIV infection. The wild-type (wt) protein binds with high affinity to mannose-rich oligosaccharides on the surface of gp120 through two quasi-symmetric sites, located in domains A and B. We recently reported on a mutant of CV-N that contained a single functional mannose-binding site, domain B, showing that multivalent binding to oligomannosides is necessary for antiviral activity. The structure of the complex with dimannose determined at 1.8 A resolution revealed a different conformation of the binding site than previously observed in the NMR structure of wt CV-N. Here, we present the 1.35 A resolution structure of the complex, which traps three different binding conformations of the site and provides experimental support for a locking and gating mechanism in the nanoscale time regime observed by molecular dynamics simulations.


===Five site mutated Cyanovirin-N with Mannose dimer bound===
Conformational gating of dimannose binding to the antiviral protein cyanovirin revealed from the crystal structure at 1.35 A resolution.,Fromme R, Katiliene Z, Fromme P, Ghirlanda G Protein Sci. 2008 May;17(5):939-44. PMID:18436959<ref>PMID:18436959</ref>


 
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 2rdk" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18436959 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_18436959}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
2RDK is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Nostoc_ellipsosporum Nostoc ellipsosporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RDK OCA].
 
==Reference==
<ref group="xtra">PMID:18436959</ref><ref group="xtra">PMID:17636873</ref><references group="xtra"/>
[[Category: Nostoc ellipsosporum]]
[[Category: Nostoc ellipsosporum]]
[[Category: Fromme, P.]]
[[Category: Fromme P]]
[[Category: Fromme, R.]]
[[Category: Fromme R]]
[[Category: Ghirlanda, G.]]
[[Category: Ghirlanda G]]
[[Category: Katiliene, Z.]]
[[Category: Katiliene Z]]
[[Category: Anti hiv]]
[[Category: Antiviral protein]]
[[Category: Cyanovirin-n]]
[[Category: Protein synthesis inhibitor]]
[[Category: Sugar binding protein]]
[[Category: X-ray diffraction]]
 
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Retrieved from "https://proteopedia.org/2rdk"