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.


1rin

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:23, 14 February 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1rin.gif|left|200px]]
 
-
<!--
+
==X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION==
-
The line below this paragraph, containing "STRUCTURE_1rin", creates the "Structure Box" on the page.
+
<StructureSection load='1rin' size='340' side='right'caption='[[1rin]], [[Resolution|resolution]] 2.60&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'>[[1rin]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RIN 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]] 2.6&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-
{{STRUCTURE_1rin| PDB=1rin | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rin FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rin OCA], [https://pdbe.org/1rin PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rin RCSB], [https://www.ebi.ac.uk/pdbsum/1rin PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rin ProSAT]</span></td></tr>
-
 
+
</table>
-
'''X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION'''
+
== Function ==
-
 
+
[https://www.uniprot.org/uniprot/LEC_PEA LEC_PEA] D-mannose specific lectin.
-
 
+
== Evolutionary Conservation ==
-
==Overview==
+
[[Image:Consurf_key_small.gif|200px|right]]
-
The x-ray crystal structure of pea lectin, in complex with a methyl glycoside of the N-linked-type oligosaccharide trimannosyl core, methyl 3,6-di-O-(alpha-D-mannopyranosyl)-alpha-D-mannopyranoside, has been solved by molecular replacement and refined at 2.6-A resolution. The R factor is 0.183 for all data in the 8.0 to 2.6 A resolution range with an average atomic temperature factor of 26.1 A2. Strong electron density for a single mannose residue is found in the monosaccharide-binding site suggesting that the trisaccharide binds primarily through one of the terminal alpha-linked mannose residues. The complex is stabilized by hydrogen bonds involving the protein residues Asp-81, Gly-99, Asn-125, Ala-217, and Glu-218, and the carbohydrate oxygen atoms O3, O4, O5, and O6. In addition, the carbohydrate makes van der Waals contacts with the protein, involving Phe-123 in particular. These interactions are very similar to those found in the monosaccharide complexes with concanavalin A and isolectin 1 of Lathyrus ochrus, confirming the structural relatedness of this family of proteins. Comparison of the pea lectin complex with the unliganded pea lectin and concanavalin A structures indicates differences in the conformation and water structure of the unliganded binding sites of these two proteins. Furthermore, a correlation between the position of the carbohydrate oxygen atoms in the complex and the bound water molecules in the unliganded binding sites is found. Binding of the trimannose core through a single terminal monosaccharide residue strongly argues that an additional fucose-binding site is responsible for the high affinity pea lectin-oligosaccharide interactions.
+
Check<jmol>
-
 
+
<jmolCheckbox>
-
==About this Structure==
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ri/1rin_consurf.spt"</scriptWhenChecked>
-
1RIN is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Pisum_sativum Pisum sativum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RIN OCA].
+
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
-
 
+
<text>to colour the structure by Evolutionary Conservation</text>
-
==Reference==
+
</jmolCheckbox>
-
X-ray crystal structure of a pea lectin-trimannoside complex at 2.6 A resolution., Rini JM, Hardman KD, Einspahr H, Suddath FL, Carver JP, J Biol Chem. 1993 May 15;268(14):10126-32. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8486683 8486683]
+
</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=1rin ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Pisum sativum]]
[[Category: Pisum sativum]]
-
[[Category: Protein complex]]
+
[[Category: Carver JP]]
-
[[Category: Carver, J P.]]
+
[[Category: Einspahr H]]
-
[[Category: Einspahr, H.]]
+
[[Category: Hardman KD]]
-
[[Category: Hardman, K D.]]
+
[[Category: Rini JM]]
-
[[Category: Rini, J M.]]
+
[[Category: Suddath FL]]
-
[[Category: Suddath, F L.]]
+
-
[[Category: Lectin]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:32:42 2008''
+

Current revision

X-RAY CRYSTAL STRUCTURE OF A PEA LECTIN-TRIMANNOSIDE COMPLEX AT 2.6 ANGSTROMS RESOLUTION

PDB ID 1rin

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/1rin"
Personal tools