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.

1n47

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Isolectin B4 from Vicia villosa in complex with the Tn antigen

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1n47"

@@ Line 1: / Line 1: @@
-[[Image:1n47.gif|left|200px]]
- {{Structure
+==Isolectin B4 from Vicia villosa in complex with the Tn antigen==
-|PDB= 1n47 |SIZE=350|CAPTION= <scene name='initialview01'>1n47</scene>, resolution 2.70&Aring;
+<StructureSection load='1n47' size='340' side='right'caption='[[1n47]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=TNR:O-(2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSYL)-L-SERINE'>TNR</scene>
+<table><tr><td colspan='2'>[[1n47]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Vicia_villosa Vicia villosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N47 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N47 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
-|GENE=
+<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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SER:SERINE'>SER</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=1n47 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n47 OCA], [https://pdbe.org/1n47 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n47 RCSB], [https://www.ebi.ac.uk/pdbsum/1n47 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n47 ProSAT]</span></td></tr>
+</table>
-'''Isolectin B4 from Vicia villosa in complex with the Tn antigen'''
+== Function ==
+[https://www.uniprot.org/uniprot/LEC_VICVI LEC_VICVI] N-acetyl-D-galactosamine specific lectin. Binds the Tn determinant (GalNAc-alpha-O-Ser/Thr) of the tumor-associated glycopeptide. Could be required for agglutinating cells such as Tn-exposed erythrocytes.
+== Evolutionary Conservation ==
-==Overview==
+[[Image:Consurf_key_small.gif|200px|right]]
-The structure of the tetrameric Vicia villosa isolectin B4 (VVLB4) in complex with a cancer antigen, the Tn glycopeptide (GalNAc-O-Ser), was determined at 2.7 A resolution. The N-acetylgalactoside moiety of the ligand binds to the primary combining site of VVLB4 in a similar way as observed for other Gal/GalNAc-specific plant lectins. The amino acid moiety of the Tn antigen is largely exposed to the solvent and makes few contacts with the protein. The structure of the complex provides a framework to understand the differences in the strength of VVLB4 binding to different sugars and emphasizes the role of a single protein residue, Tyr127, as a structural determinant of Tn-binding specificity.
+Check<jmol>
+  <jmolCheckbox>
-==About this Structure==
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n4/1n47_consurf.spt"</scriptWhenChecked>
-N47 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Vicia_villosa Vicia villosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N47 OCA].
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
-==Reference==
+  </jmolCheckbox>
-The crystal structure of a plant lectin in complex with the Tn antigen., Babino A, Tello D, Rojas A, Bay S, Osinaga E, Alzari PM, FEBS Lett. 2003 Feb 11;536(1-3):106-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12586347 12586347]
+</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=1n47 ConSurf].
-[[Category: Protein complex]]
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Vicia villosa]]
-[[Category: Alzari, P M.]]
+[[Category: Alzari PM]]
-[[Category: Babino, A.]]
+[[Category: Babino A]]
-[[Category: Bay, S.]]
+[[Category: Bay S]]
-[[Category: Osinaga, E.]]
+[[Category: Osinaga E]]
-[[Category: Rojas, A.]]
+[[Category: Rojas A]]
-[[Category: Tello, D.]]
+[[Category: Tello D]]
-[[Category: CA]]
-[[Category: MN]]
-[[Category: TNR]]
-[[Category: cancer antigen]]
-[[Category: carbohydrate recognition]]
-[[Category: glycoprotein tn-binding protein]]
-[[Category: vicia villosa lectin]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:51:56 2008''

1n47

From Proteopedia

Current revision

Isolectin B4 from Vicia villosa in complex with the Tn antigen

Structural highlights

Function

Evolutionary Conservation

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox