2nmn: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2nmn.png|left|200px]]
-<!--
+==Crystal structure of human galectin-3 carbohydrate-recognising domain at 2.45 angstrom resolution==
-The line below this paragraph, containing "STRUCTURE_2nmn", creates the "Structure Box" on the page.
+<StructureSection load='2nmn' size='340' side='right'caption='[[2nmn]], [[Resolution|resolution]] 2.45&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'>[[2nmn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NMN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NMN 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]] 2.45&#8491;</td></tr>
--->
+<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=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=PRD_900004:beta-lactose'>PRD_900004</scene></td></tr>
-{{STRUCTURE_2nmn|  PDB=2nmn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nmn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nmn OCA], [https://pdbe.org/2nmn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nmn RCSB], [https://www.ebi.ac.uk/pdbsum/2nmn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nmn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/LEG3_HUMAN LEG3_HUMAN] Galactose-specific lectin which binds IgE. May mediate with the alpha-3, beta-1 integrin the stimulation by CSPG4 of endothelial cells migration. Together with DMBT1, required for terminal differentiation of columnar epithelial cells during early embryogenesis (By similarity). In the nucleus: acts as a pre-mRNA splicing factor. Involved in acute inflammatory responses including neutrophil activation and adhesion, chemoattraction of monocytes macrophages, opsonization of apoptotic neutrophils, and activation of mast cells.<ref>PMID:15181153</ref> <ref>PMID:19594635</ref> <ref>PMID:19616076</ref>
+== 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/nm/2nmn_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=2nmn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Galectin-3 is a multifunctional carbohydrate-binding protein that has roles in cancer progression. In addition to carbohydrate-dependent extracellular functions, galectin-3 participates in carbohydrate-independent intracellular signalling pathways, including apoptosis, via protein-protein interactions, some of which engage the carbohydrate-binding groove. When ligands bind within this site, conformational rearrangements are induced and information on unliganded galectin-3 is therefore valuable for structure-based drug design. Removal of cocrystallized lactose from the human galectin-3 carbohydrate-recognition domain was achieved via crystal soaking, but took weeks despite low affinity. Pre-soaking to remove lactose enabled the subsequent binding of cryoprotectant glycerol, whereas when the lactose was not removed a priori the glycerol could not displace it in the short cryosoaking time frame. This slow diffusion of lactose out of the crystals contrasts with the entrance of glycerol, which takes place within minutes. The importance of the removal of incumbent ligands prior to attempts to introduce alternative ligands is indicated, even for proteins exhibiting low affinity for ligands, and has significance for ligand exchange in structure-based drug design.
-===Crystal structure of human galectin-3 carbohydrate-recognising domain at 2.45 angstrom resolution===
+Slow diffusion of lactose out of galectin-3 crystals monitored by X-ray crystallography: possible implications for ligand-exchange protocols.,Collins PM, Hidari KI, Blanchard H Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):415-9. Epub 2007, Feb 21. PMID:17327679<ref>PMID:17327679</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2nmn" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17327679}}, adds the Publication Abstract to the page
+*[[Galectin 3D structures|Galectin 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17327679 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17327679}}
+__TOC__
+</StructureSection>
-==About this Structure==
-NMN is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NMN OCA].
-==Reference==
-Slow diffusion of lactose out of galectin-3 crystals monitored by X-ray crystallography: possible implications for ligand-exchange protocols., Collins PM, Hidari KI, Blanchard H, Acta Crystallogr D Biol Crystallogr. 2007 Mar;63(Pt 3):415-9. Epub 2007, Feb 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17327679 17327679]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Blanchard, H.]]
+[[Category: Blanchard H]]
-[[Category: Collins, P M.]]
+[[Category: Collins PM]]
-[[Category: Beta sandwich]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 23:08:56 2008''