1ugx: Difference between revisions

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[[Image:1ugx.png|left|200px]]
==Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex==
<StructureSection load='1ugx' size='340' side='right' caption='[[1ugx]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ugx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Artocarpus_integer Artocarpus integer]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UGX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UGX FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene><br>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MGC:ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE'>MGC</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1m26|1m26]], [[1jac|1jac]], [[1ugw|1ugw]], [[1ugy|1ugy]], [[1uh0|1uh0]], [[1uh1|1uh1]]</td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ugx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ugx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ugx RCSB], [http://www.ebi.ac.uk/pdbsum/1ugx PDBsum]</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/ug/1ugx_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/chain_selection.php?pdb_ID=2ata ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry. O-H..., centered pi and C-H...pi hydrogen bonds involving this site also exist. On the other hand, beta-substitution leads to severe steric clashes. Therefore, in complexes involving beta-linked disaccharides, the reducing sugar binds at the primary site with the non-reducing end located at secondary site B. The interactions at secondary site B are primarily through water bridges. Thus, the nature of the linkage determines the mode of the association of the sugar with jacalin. The interactions observed in the crystal structures and modeling based on them provide a satisfactory qualitative explanation of the available thermodynamic data on jacalin-carbohydrate interactions. They also lead to fresh insights into the nature of the binding of glycoproteins by jacalin.


{{STRUCTURE_1ugx|  PDB=1ugx  |  SCENE=  }}
Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study.,Jeyaprakash AA, Katiyar S, Swaminathan CP, Sekar K, Surolia A, Vijayan M J Mol Biol. 2003 Sep 5;332(1):217-28. PMID:12946359<ref>PMID:12946359</ref>


===Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_12946359}}
== References ==
 
<references/>
==About this Structure==
__TOC__
[[1ugx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Artocarpus_integer Artocarpus integer]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UGX OCA].
</StructureSection>
 
==Reference==
<ref group="xtra">PMID:012946359</ref><references group="xtra"/>
[[Category: Artocarpus integer]]
[[Category: Artocarpus integer]]
[[Category: Jeyaprakash, A A.]]
[[Category: Jeyaprakash, A A.]]

Revision as of 22:00, 29 September 2014

Crystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complexCrystal structure of jacalin- Me-alpha-T-antigen (Gal-beta(1-3)-GalNAc-alpha-o-Me) complex

Structural highlights

1ugx is a 2 chain structure with sequence from Artocarpus integer. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Related:1m26, 1jac, 1ugw, 1ugy, 1uh0, 1uh1
Resources:FirstGlance, OCA, RCSB, PDBsum

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 structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry. O-H..., centered pi and C-H...pi hydrogen bonds involving this site also exist. On the other hand, beta-substitution leads to severe steric clashes. Therefore, in complexes involving beta-linked disaccharides, the reducing sugar binds at the primary site with the non-reducing end located at secondary site B. The interactions at secondary site B are primarily through water bridges. Thus, the nature of the linkage determines the mode of the association of the sugar with jacalin. The interactions observed in the crystal structures and modeling based on them provide a satisfactory qualitative explanation of the available thermodynamic data on jacalin-carbohydrate interactions. They also lead to fresh insights into the nature of the binding of glycoproteins by jacalin.

Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study.,Jeyaprakash AA, Katiyar S, Swaminathan CP, Sekar K, Surolia A, Vijayan M J Mol Biol. 2003 Sep 5;332(1):217-28. PMID:12946359[1]

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

References

  1. ↑ Jeyaprakash AA, Katiyar S, Swaminathan CP, Sekar K, Surolia A, Vijayan M. Structural basis of the carbohydrate specificities of jacalin: an X-ray and modeling study. J Mol Biol. 2003 Sep 5;332(1):217-28. PMID:12946359

1ugx, resolution 1.60Å

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