2dvg: Difference between revisions

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{{Seed}}
[[Image:2dvg.png|left|200px]]


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==Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC complex==
The line below this paragraph, containing "STRUCTURE_2dvg", creates the "Structure Box" on the page.
<StructureSection load='2dvg' size='340' side='right'caption='[[2dvg]], [[Resolution|resolution]] 2.78&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'>[[2dvg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arachis_hypogaea Arachis hypogaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DVG 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]] 2.78&#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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLA:ALPHA+D-GALACTOSE'>GLA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_2dvg|  PDB=2dvg  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dvg OCA], [https://pdbe.org/2dvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dvg RCSB], [https://www.ebi.ac.uk/pdbsum/2dvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dvg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/LECG_ARAHY LECG_ARAHY] D-galactose 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/dv/2dvg_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=2dvg ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K. The use of water bridges as a strategy for generating carbohydrate specificity was previously deduced from the complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen (Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed analysis of lectin-sugar interactions in the complexes shows that they are more extensive when the beta-anomer is involved in the linkage. As expected, the second sugar residue is ill-defined when the linkage is 1--&gt;6. There are more than two dozen water molecules which occur in the hydration shells of all structures determined at resolutions better than 2.5 A. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin-sugar interactions are also substantially conserved. The lectin molecule is fairly rigid and does not appear to be affected by changes in temperature.


===Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC complex===
Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin.,Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1413-21. Epub 2006, Oct 18. PMID:17057347<ref>PMID:17057347</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2dvg" style="background-color:#fffaf0;"></div>


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==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_17057347}}, adds the Publication Abstract to the page
*[[Agglutinin 3D structures|Agglutinin 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 17057347 is the PubMed ID number.
*[[Galactose-binding lectin|Galactose-binding lectin]]
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== References ==
{{ABSTRACT_PUBMED_17057347}}
<references/>
 
__TOC__
==About this Structure==
</StructureSection>
2DVG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Arachis_hypogaea Arachis hypogaea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DVG OCA].
 
==Reference==
Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin., Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M, Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1413-21. Epub 2006, Oct 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17057347 17057347]
 
Crystal structure of peanut lectin, a protein with an unusual quaternary structure., Banerjee R, Mande SC, Ganesh V, Das K, Dhanaraj V, Mahanta SK, Suguna K, Surolia A, Vijayan M, Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):227-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8278370 8278370]
 
Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex., Banerjee R, Das K, Ravishankar R, Suguna K, Surolia A, Vijayan M, J Mol Biol. 1996 Jun 7;259(2):281-96. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8656429 8656429]
 
Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure., Kundhavai Natchiar S, Arockia Jeyaprakash A, Ramya TN, Thomas CJ, Suguna K, Surolia A, Vijayan M, Acta Crystallogr D Biol Crystallogr. 2004 Feb;60(Pt 2):211-9. Epub 2004, Jan 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14747696 14747696]
[[Category: Arachis hypogaea]]
[[Category: Arachis hypogaea]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Jayaraman, N.]]
[[Category: Jayaraman N]]
[[Category: Mitra, N.]]
[[Category: Mitra N]]
[[Category: Natchiar, S K.]]
[[Category: Natchiar SK]]
[[Category: Srinivas, O.]]
[[Category: Srinivas O]]
[[Category: Surolia, A.]]
[[Category: Surolia A]]
[[Category: Vijayan, M.]]
[[Category: Vijayan M]]
[[Category: Agglutinin]]
[[Category: Carbohydrate specificity]]
[[Category: Legume lectin]]
[[Category: Open quaternary structure]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:11:14 2008''

Latest revision as of 11:30, 25 October 2023

Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC complexCrystal structure of peanut lectin GAL-ALPHA-1,6-GLC complex

Structural highlights

2dvg is a 4 chain structure with sequence from Arachis hypogaea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.78Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LECG_ARAHY D-galactose specific lectin.

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

Crystal structures of peanut lectin complexed with Galbeta1-3Gal, methyl-T-antigen, Galbeta1-6GalNAc, Galalpha1-3Gal and Galalpha1-6Glc and that of a crystal grown in the presence of Galalpha1-3Galbeta1-4Gal have been determined using data collected at 100 K. The use of water bridges as a strategy for generating carbohydrate specificity was previously deduced from the complexes of the lectin with lactose (Galbeta1-4Glc) and T-antigen (Galbeta1-3GalNAc). This has been confirmed by the analysis of the complexes with Galbeta1-3Gal and methyl-T-antigen (Galbeta1-3GalNAc-alpha-OMe). A detailed analysis of lectin-sugar interactions in the complexes shows that they are more extensive when the beta-anomer is involved in the linkage. As expected, the second sugar residue is ill-defined when the linkage is 1-->6. There are more than two dozen water molecules which occur in the hydration shells of all structures determined at resolutions better than 2.5 A. Most of them are involved in stabilizing the structure, particularly loops. Water molecules involved in lectin-sugar interactions are also substantially conserved. The lectin molecule is fairly rigid and does not appear to be affected by changes in temperature.

Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin.,Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1413-21. Epub 2006, Oct 18. PMID:17057347[1]

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

See Also

References

  1. ↑ Natchiar SK, Srinivas O, Mitra N, Surolia A, Jayaraman N, Vijayan M. Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin. Acta Crystallogr D Biol Crystallogr. 2006 Nov;62(Pt 11):1413-21. Epub 2006, Oct 18. PMID:17057347 doi:10.1107/S0907444906035712

2dvg, resolution 2.78Å

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