3lm1: Difference between revisions
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== | ==Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc== | ||
[[http://www.uniprot.org/uniprot/LECA_MACPO LECA_MACPO | <StructureSection load='3lm1' size='340' side='right'caption='[[3lm1]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3lm1]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Maclura_pomifera Maclura pomifera]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LM1 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]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LEC:N-[(2S,3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-2-(4-NITROPHENOXY)OXAN-3-YL]ETHANAMIDE'>LEC</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=3lm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lm1 OCA], [https://pdbe.org/3lm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3lm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lm1 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/LECA_MACPO LECA_MACPO] D-galactose-specific lectin, binds the T-antigen structure Gal-beta1,3-GalNAc. | |||
== 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/lm/3lm1_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=3lm1 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The Maclura pomifera agglutinin (MPA) recognizes the T-antigen disaccharide Galbeta1,3GalNAc mainly through interaction of the alpha-GalNAc moiety with its primary site, but the interactions of the two flanking subsites A and B with aglycones and substituents other than Gal, respectively, are not well understood. We therefore characterized the specificity of MPA in more detail by glycan micro-array analysis and determined the crystal structures of MPA without ligand and in complexes with Galbeta1,3GalNAc and p-nitrophenyl alpha-GalNAc. In both sugar complexes, pairs of ligands created inter-tetramer hydrogen-bond bridging networks. While subsite A showed increased affinity for hydrophobic aglycones, it also accommodated several sugar substituents. Notably, a GalNAc-O-tripeptide, a Tn antigen mimic, showed lower affinity than these compounds in surface plasmon resonance experiments. The glycan array data showed subsite B accepted compounds in which the O3 position of the GalNAc was substituted with various sugars other than Gal, but substitutions at O6 led to inactivity. Additions to the Gal moiety of the disaccharide also had only small effects on reactivity. These results are all compatible with the features seen in the crystal structures. | |||
Characterization of the secondary binding sites of Maclura pomifera agglutinin by glycan array and crystallographic analyses.,Huang J, Xu Z, Wang D, Ogata CM, Palczewski K, Lee X, Young NM Glycobiology. 2010 Sep 8. PMID:20826825<ref>PMID:20826825</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
< | </div> | ||
<div class="pdbe-citations 3lm1" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Agglutinin 3D structures|Agglutinin 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Maclura pomifera]] | [[Category: Maclura pomifera]] | ||
[[Category: Hazen | [[Category: Hazen SL]] | ||
[[Category: Hirama | [[Category: Hirama T]] | ||
[[Category: Huang | [[Category: Huang J]] | ||
[[Category: Lee | [[Category: Lee X]] | ||
[[Category: Ogato | [[Category: Ogato C]] | ||
[[Category: Palczewski | [[Category: Palczewski K]] | ||
[[Category: Wang | [[Category: Wang D]] | ||
[[Category: Xu | [[Category: Xu Z]] | ||
[[Category: Young | [[Category: Young NM]] | ||
Latest revision as of 08:40, 6 September 2023
Crystal Structure Analysis of Maclura pomifera agglutinin complex with p-nitrophenyl-GalNAc
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