1nc2: Difference between revisions

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-{{Seed}}
-[[Image:1nc2.png|left|200px]]
-<!--
+==Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y-DOTA==
-The line below this paragraph, containing "STRUCTURE_1nc2", creates the "Structure Box" on the page.
+<StructureSection load='1nc2' size='340' side='right'caption='[[1nc2]], [[Resolution|resolution]] 2.10&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'>[[1nc2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NC2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NC2 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]] 2.1&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DOE:(S)-2-(4-(2-(2-HYDROXYETHYLTHIO)-ACETAMIDO)-BENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N,N,N-TETRAACETATE'>DOE</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene></td></tr>
-{{STRUCTURE_1nc2|  PDB=1nc2  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nc2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nc2 OCA], [https://pdbe.org/1nc2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nc2 RCSB], [https://www.ebi.ac.uk/pdbsum/1nc2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nc2 ProSAT]</span></td></tr>
+</table>
+== 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/nc/1nc2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1nc2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the crystal structures of antibody 2D12.5 Fab bound to an yttrium-DOTA analogue and separately to a gadolinium-DOTA analogue. The rare earth elements have many useful properties as probes, and 2D12.5 binds the DOTA (1,4,7,10-tetraazacyclododecane-N,N',N' ',N' "-tetraacetic acid) complexes of all of them (Corneillie et al. J. Am. Chem. Soc. 2003, 125, 3436-3437). The structures show that there are no direct protein-metal interactions: a bridging water acts as a link between the protein and metal, with the chelate present as the M isomer in each case. DOTA forms an amphipathic cylinder with the charged carboxylate groups toward the face of the chelate near the metal ion, while nonpolar methylene groups from the macrocycle and the carboxymethyl groups occupy the rear and sides of the molecule. The orientation of the metal-DOTA in the 2D12.5 complex places most of the methylene carbon atoms of DOTA in hydrophobic contact with aromatic protein side chains. Other binding interactions between the metal complex and the antibody include a bidentate salt bridge, four direct H-bonds, and four to five water-mediated H-bonds. We find that 2D12.5 exhibits enantiomeric binding generality, binding yttrium chelates in both Lambda(deltadeltadeltadelta) and Delta(lambdalambdalambdalambda) configurations with modestly different affinities. This develops from the symmetrical nature of the DOTA chelate, which places heteroatoms and hydrophobic atoms in approximately the same relative positions regardless of the helicity of DOTA.
-===Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Y-DOTA===
+Crystal structures of two complexes of the rare-earth-DOTA-binding antibody 2D12.5: ligand generality from a chiral system.,Corneillie TM, Fisher AJ, Meares CF J Am Chem Soc. 2003 Dec 10;125(49):15039-48. PMID:14653738<ref>PMID:14653738</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1nc2" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_14653738}}, adds the Publication Abstract to the page
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 14653738 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_14653738}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NC2 OCA].
+[[Category: Mus musculus]]
+[[Category: Corneillie TM]]
-==Reference==
+[[Category: Fisher AJ]]
-Crystal structures of two complexes of the rare-earth-DOTA-binding antibody 2D12.5: ligand generality from a chiral system., Corneillie TM, Fisher AJ, Meares CF, J Am Chem Soc. 2003 Dec 10;125(49):15039-48. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14653738 14653738]
+[[Category: Meares CF]]
-[[Category: Corneillie, T M.]]
-[[Category: Fisher, A J.]]
-[[Category: Meares, C F.]]
-[[Category: Antibody-dota complex]]
-[[Category: Dota]]
-[[Category: Gamma turn]]
-[[Category: Metal chelate]]
-[[Category: N-linked glycosylation]]
-[[Category: Rare earth]]
-[[Category: Yttrium]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 06:07:12 2008''