1uz6: Difference between revisions

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{{Seed}}
[[Image:1uz6.png|left|200px]]


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==anti-Lewis X Fab fragment uncomplexed==
The line below this paragraph, containing "STRUCTURE_1uz6", creates the "Structure Box" on the page.
<StructureSection load='1uz6' size='340' side='right'caption='[[1uz6]], [[Resolution|resolution]] 2.05&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'>[[1uz6]] is a 8 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=1UZ6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UZ6 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]] 2.05&#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=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_1uz6|  PDB=1uz6  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1uz6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uz6 OCA], [https://pdbe.org/1uz6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uz6 RCSB], [https://www.ebi.ac.uk/pdbsum/1uz6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uz6 ProSAT]</span></td></tr>
</table>
== 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/uz/1uz6_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=1uz6 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Lewis X trisaccharide is pivotal in mediating specific cell-cell interactions. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, has been shown to recognize the Lewis X trisaccharide. Here we describe the structure of the Fab fragment of 291-2G3-A, with Lewis X, to 1.8 A resolution. The crystallographic analysis revealed that the antigen binding site is a rather shallow binding pocket, and residues from all six complementary determining regions of the antibody contact all sugar residues. The high specificity of the binding pocket does not result in high affinity; the K(D) determined by isothermal calorimetry is 11 microM. However, this affinity is in the same range as for other sugar-antibody complexes. The detailed understanding of the antibody-Lewis X interaction revealed by the crystal structure may be helpful in the design of better diagnostic tools for schistosomiasis and for studying Lewis X-mediated cell-cell interactions by antibody interference.


===ANTI-LEWIS X FAB FRAGMENT UNCOMPLEXED===
Structure of an anti-Lewis X Fab fragment in complex with its Lewis X antigen.,van Roon AM, Pannu NS, de Vrind JP, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP Structure. 2004 Jul;12(7):1227-36. PMID:15242599<ref>PMID:15242599</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1uz6" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_15242599}}, adds the Publication Abstract to the page
*[[Antibody 3D structures|Antibody 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 15242599 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_15242599}}
== References ==
 
<references/>
==About this Structure==
__TOC__
1UZ6 is a [[Single protein]] structure of sequence 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=1UZ6 OCA].
</StructureSection>
 
[[Category: Large Structures]]
==Reference==
Structure of an anti-Lewis X Fab fragment in complex with its Lewis X antigen., van Roon AM, Pannu NS, de Vrind JP, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP, Structure. 2004 Jul;12(7):1227-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15242599 15242599]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Single protein]]
[[Category: Abrahams JP]]
[[Category: Abrahams, J P.]]
[[Category: De Vrind JPM]]
[[Category: Boom, J H.Van.]]
[[Category: Deelder AM]]
[[Category: Deelder, A M.]]
[[Category: Hokke CH]]
[[Category: Hokke, C H.]]
[[Category: Pannu NS]]
[[Category: Marel, G A.Van Der.]]
[[Category: Van Boom JH]]
[[Category: Pannu, N S.]]
[[Category: Van Der marel GA]]
[[Category: Roon, A M.M Van.]]
[[Category: Van Roon AMM]]
[[Category: Vrind, J P.M De.]]
[[Category: Anti-carbohydrate]]
[[Category: Antibody]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 10:11:06 2008''

Latest revision as of 16:04, 13 December 2023

anti-Lewis X Fab fragment uncomplexedanti-Lewis X Fab fragment uncomplexed

Structural highlights

1uz6 is a 8 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.05Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The Lewis X trisaccharide is pivotal in mediating specific cell-cell interactions. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, has been shown to recognize the Lewis X trisaccharide. Here we describe the structure of the Fab fragment of 291-2G3-A, with Lewis X, to 1.8 A resolution. The crystallographic analysis revealed that the antigen binding site is a rather shallow binding pocket, and residues from all six complementary determining regions of the antibody contact all sugar residues. The high specificity of the binding pocket does not result in high affinity; the K(D) determined by isothermal calorimetry is 11 microM. However, this affinity is in the same range as for other sugar-antibody complexes. The detailed understanding of the antibody-Lewis X interaction revealed by the crystal structure may be helpful in the design of better diagnostic tools for schistosomiasis and for studying Lewis X-mediated cell-cell interactions by antibody interference.

Structure of an anti-Lewis X Fab fragment in complex with its Lewis X antigen.,van Roon AM, Pannu NS, de Vrind JP, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP Structure. 2004 Jul;12(7):1227-36. PMID:15242599[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ van Roon AM, Pannu NS, de Vrind JP, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP. Structure of an anti-Lewis X Fab fragment in complex with its Lewis X antigen. Structure. 2004 Jul;12(7):1227-36. PMID:15242599 doi:10.1016/j.str.2004.05.008

1uz6, resolution 2.05Å

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