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New page: left|200px<br /><applet load="5cna" size="450" color="white" frame="true" align="right" spinBox="true" caption="5cna, resolution 2.0Å" /> '''REFINED STRUCTURE OF ...
 
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[[Image:5cna.gif|left|200px]]<br /><applet load="5cna" size="450" color="white" frame="true" align="right" spinBox="true"
caption="5cna, resolution 2.0&Aring;" />
'''REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE'''<br />


==Overview==
==REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE==
The three-dimensional structure of the complex between methyl, alpha-D-mannopyranoside and concanavalin A has been refined at 2.0 A, resolution. Diffraction data were recorded from a single crystal (space, group P2(1)2(1)2(1), a = 123.7, b = 128.6, c = 67.2 A) using synchrotron, radiation at a wavelength of 1.488 A. The final model has good geometry, and an R factor of 19.9% for 58 871 reflections (82% complete), within the, resolution limits of 8 to 2 A, with F &gt; 1.0sigma(F). The asymmetric unit, contains four protein subunits arranged as a dimer of dimers with, approximate 222 point symmetry. Each monomer binds one saccharide, molecule. Each sugar is bound to the protein by hydrogen bonds and van der, Waals contacts. Although the four subunits are not crystallographically, equivalent, the protein-saccharide interactions are nearly identical in, each of the four binding sites. The differences that do occur between the, four sites are in the structure of the water network which surrounds each, saccharide; these networks are involved in crystal packing. The structure, of the complex is compared with a refined saccharide-free concanavalin A, structure. The saccharide-free structure is composed of, crystallographically identical subunits, again assembled as a dimer of, dimers, but with exact 222 symmetry. In the saccharide complex the, tetramer association is different in that the monomers tend to separate, resulting in fewer intersubunit interactions. The average temperature, factor of the mannoside complex is considerably higher than that of the, saccharide-free protein. The binding site in the saccharide-free structure, is occupied by three ordered water molecules and the side chain of Asp71, from a neighbouring molecule in the crystal. These occupy positions, similar to those of the four saccharide hydroxyls which are hydrogen, bonded to the site. Superposition of the saccharide-binding site from each, structure shows that the major changes on binding involve expulsion of, these ordered solvents and the reorientation of the side chain of Tyrl00., Overall the surface accessibility of the saccharide decreases from 370 to, 100 A(2) when it binds to the protein. This work builds upon the earlier, studies of Derewenda et al. [Derewenda, Yariv, Helliwell, Kalb (Gilboa), Dodson, Papiz, Wan &amp; Campbell (1989). EMBO J. 8, 2198-2193] at 2.9 A, resolution, which was the first detailed study of lectin-saccharide, interactions.
<StructureSection load='5cna' size='340' side='right'caption='[[5cna]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5cna]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4cna 4cna]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CNA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CNA 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MMA:O1-METHYL-MANNOSE'>MMA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5cna FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cna OCA], [https://pdbe.org/5cna PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cna RCSB], [https://www.ebi.ac.uk/pdbsum/5cna PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cna ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CONA_CANEN CONA_CANEN] D-mannose specific lectin.
== 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/cn/5cna_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=5cna ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
5CNA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Canavalia_ensiformis Canavalia ensiformis] with MMA, MN, CA and CL as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 4CNA. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=5CNA OCA].
*[[Concanavalin 3D structures|Concanavalin 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Refined structure of concanavalin A complexed with methyl alpha-D-mannopyranoside at 2.0 A resolution and comparison with the saccharide-free structure., Naismith JH, Emmerich C, Habash J, Harrop SJ, Helliwell JR, Hunter WN, Raftery J, Kalb AJ, Yariv J, Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):847-58. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15299352 15299352]
[[Category: Canavalia ensiformis]]
[[Category: Canavalia ensiformis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Emmerich, C.]]
[[Category: Emmerich C]]
[[Category: Gilboa, A.J.Kalb.]]
[[Category: Habash J]]
[[Category: Habash, J.]]
[[Category: Harrop SJ]]
[[Category: Harrop, S.J.]]
[[Category: Helliwell JR]]
[[Category: Helliwell, J.R.]]
[[Category: Hunter WN]]
[[Category: Hunter, W.N.]]
[[Category: Naismith JH]]
[[Category: Naismith, J.H.]]
[[Category: Raftery J]]
[[Category: Raftery, J.]]
[[Category: Yariv J]]
[[Category: Yariv, J.]]
[[Category: CA]]
[[Category: CL]]
[[Category: MMA]]
[[Category: MN]]
[[Category: lectin(agglutinin)]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:26:23 2007''

Latest revision as of 12:20, 6 March 2024

REFINED STRUCTURE OF CONCANAVALIN A COMPLEXED WITH ALPHA-METHYL-D-MANNOPYRANOSIDE AT 2.0 ANGSTROMS RESOLUTION AND COMPARISON WITH THE SACCHARIDE-FREE STRUCTURE

5cna, resolution 2.00Å

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