This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2dty

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="2dty" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dty, resolution 2.65&Aring;" /> '''Crystal structure of...)
Current revision (08:30, 25 October 2023) (edit) (undo)
 
(16 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2dty.gif|left|200px]]<br /><applet load="2dty" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2dty, resolution 2.65&Aring;" />
 
-
'''Crystal structure of basic winged bean lectin complexed with N-acetyl-D-galactosamine'''<br />
 
-
==Overview==
+
==Crystal structure of basic winged bean lectin complexed with N-acetyl-D-galactosamine==
-
The crystal structure of the complexes of basic winged-bean lectin with, galactose, 2-methoxygalactose, N-acetylgalactosamine and, methyl-alpha-N-acetylgalactosamine have been determined. Lectin-sugar, interactions involve four hydrogen bonds and a stacking interaction in all, of the complexes. In addition, an N-H...O hydrogen bond involving the, hydroxyl group at C2 exists in the galactose and 2-methoxygalactose, complexes. An additional hydrophobic interaction involving the methyl, group in the latter leads to the higher affinity of the methyl derivative., In the lectin-N-acetylgalactosamine complex the N-H...O hydrogen bond is, lost, but a compensatory hydrogen bond is formed involving the O atom of, the acetamido group. In addition, the CH(3) moiety of the acetamido group, is involved in hydrophobic interactions. Consequently, the 2-methyl and, acetamido derivatives of galactose have nearly the same affinity for the, lectin. The methyl group alpha-linked to the galactose takes part in, additional hydrophobic interactions. Therefore, methyl-alpha-N-acetylgalactosamine has a higher affinity than, N-acetylgalactosamine for the lectin. The structures of basic winged-bean, lectin-sugar complexes provide a framework for examining the relative, affinity of galactose and galactosamine for the lectins that bind to them., The complexes also lead to a structural explanation for the blood-group, specificity of basic winged-bean lectin.
+
<StructureSection load='2dty' size='340' side='right'caption='[[2dty]], [[Resolution|resolution]] 2.65&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2dty]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Psophocarpus_tetragonolobus Psophocarpus tetragonolobus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DTY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DTY 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]] 2.65&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2G:N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE'>A2G</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=FUL:BETA-L-FUCOSE'>FUL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2dty FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dty OCA], [https://pdbe.org/2dty PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dty RCSB], [https://www.ebi.ac.uk/pdbsum/2dty PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dty ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LEC1_PSOTE LEC1_PSOTE] 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/dt/2dty_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=2dty ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The crystal structure of the complexes of basic winged-bean lectin with galactose, 2-methoxygalactose, N-acetylgalactosamine and methyl-alpha-N-acetylgalactosamine have been determined. Lectin-sugar interactions involve four hydrogen bonds and a stacking interaction in all of the complexes. In addition, an N-H...O hydrogen bond involving the hydroxyl group at C2 exists in the galactose and 2-methoxygalactose complexes. An additional hydrophobic interaction involving the methyl group in the latter leads to the higher affinity of the methyl derivative. In the lectin-N-acetylgalactosamine complex the N-H...O hydrogen bond is lost, but a compensatory hydrogen bond is formed involving the O atom of the acetamido group. In addition, the CH(3) moiety of the acetamido group is involved in hydrophobic interactions. Consequently, the 2-methyl and acetamido derivatives of galactose have nearly the same affinity for the lectin. The methyl group alpha-linked to the galactose takes part in additional hydrophobic interactions. Therefore, methyl-alpha-N-acetylgalactosamine has a higher affinity than N-acetylgalactosamine for the lectin. The structures of basic winged-bean lectin-sugar complexes provide a framework for examining the relative affinity of galactose and galactosamine for the lectins that bind to them. The complexes also lead to a structural explanation for the blood-group specificity of basic winged-bean lectin.
-
==About this Structure==
+
Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc.,Kulkarni KA, Katiyar S, Surolia A, Vijayan M, Suguna K Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1319-24. Epub 2006, Oct 18. PMID:17057334<ref>PMID:17057334</ref>
-
2DTY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Psophocarpus_tetragonolobus Psophocarpus tetragonolobus] with A2G, MN and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2DTY OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
Structural basis for the carbohydrate-specificity of basic winged-bean lectin and its differential affinity for Gal and GalNAc., Kulkarni KA, Katiyar S, Surolia A, Vijayan M, Suguna K, Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1319-24. Epub 2006, Oct 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17057334 17057334]
+
</div>
-
[[Category: Psophocarpus tetragonolobus]]
+
<div class="pdbe-citations 2dty" style="background-color:#fffaf0;"></div>
-
[[Category: Single protein]]
+
-
[[Category: Katiyar, S.]]
+
-
[[Category: Kulkarni, K.A.]]
+
-
[[Category: Suguna, K.]]
+
-
[[Category: Surolia, A.]]
+
-
[[Category: Vijayan, M.]]
+
-
[[Category: A2G]]
+
-
[[Category: CA]]
+
-
[[Category: MN]]
+
-
[[Category: agglutinin]]
+
-
[[Category: glycosylated protein]]
+
-
[[Category: legume lectin]]
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:46:48 2007''
+
==See Also==
 +
*[[Agglutinin 3D structures|Agglutinin 3D structures]]
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
 +
[[Category: Psophocarpus tetragonolobus]]
 +
[[Category: Katiyar S]]
 +
[[Category: Kulkarni KA]]
 +
[[Category: Suguna K]]
 +
[[Category: Surolia A]]
 +
[[Category: Vijayan M]]

Current revision

Crystal structure of basic winged bean lectin complexed with N-acetyl-D-galactosamine

PDB ID 2dty

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2dty"
Personal tools