3bd4: Difference between revisions

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

OCA

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-[[Image:3bd4.jpg|left|200px]]
- {{Structure
+==Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals==
-|PDB= 3bd4 |SIZE=350|CAPTION= <scene name='initialview01'>3bd4</scene>, resolution 2.4&Aring;
+<StructureSection load='3bd4' size='340' side='right'caption='[[3bd4]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Cd+Binding+Site+For+Residue+B+1'>AC1</scene>, <scene name='pdbsite=AC2:Cd+Binding+Site+For+Residue+A+2'>AC2</scene> and <scene name='pdbsite=AC3:Btb+Binding+Site+For+Residue+A+1'>AC3</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>
+<table><tr><td colspan='2'>[[3bd4]] is a 2 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=3BD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BD4 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]] 2.4&#8491;</td></tr>
-|GENE= 3d8 vl ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></td></tr>
-|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd00099 IGv], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07686 V-set]</span>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bd4 OCA], [https://pdbe.org/3bd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bd4 RCSB], [https://www.ebi.ac.uk/pdbsum/3bd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bd4 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[3bd3|3BD3]], [[3bd5|3BD5]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bd4 OCA], [http://www.ebi.ac.uk/pdbsum/3bd4 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bd4 RCSB]</span>
+== 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/bd/3bd4_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=3bd4 ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of single domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals'''
+==See Also==
+*[[Antibody 3D structures|Antibody 3D structures]]
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-==About this Structure==
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-BD4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BD4 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Crystal structure of single-domain VL of an anti-DNA binding antibody 3D8 scFv and its active site revealed by complex structures of a small molecule and metals., Park SY, Lee WR, Lee SC, Kwon MH, Kim YS, Kim JS, Proteins. 2008 Mar 12;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18338383 18338383]
 [[Category: Mus musculus]]
-[[Category: Single protein]]
+[[Category: Kim JS]]
-[[Category: Kim, J S.]]
+[[Category: Park SK]]
-[[Category: Park, S K.]]
-[[Category: beta sandwich]]
-[[Category: immune system]]
-[[Category: metal]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:59:15 2008''