2d5x: 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:2d5x.gif|left|200px]]<br />
-<applet load="2d5x" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2d5x, resolution 1.45&Aring;" />
-'''Crystal structure of carbonmonoxy horse hemoglobin complexed with L35'''<br />
-==Overview==
+==Crystal structure of carbonmonoxy horse hemoglobin complexed with L35==
-Although detailed crystal structures of haemoglobin (Hb) provide a clear, understanding of the basic allosteric mechanism of the protein, and how, this in turn controls oxygen affinity, recent experiments with artificial, effector molecules have shown a far greater control of oxygen binding than, with natural heterotropic effectors. Contrary to the established text-book, view, these non-physiological compounds are able to reduce oxygen affinity, very strongly without switching the protein to the T (tense) state. In an, earlier paper we showed that bezafibrate (BZF) binds to a surface pocket, on the alpha subunits of R state Hb, strongly reducing the oxygen affinity, of this protein conformation. Here we report the crystallisation of Hb, with L35, a related compound, and show that this binds to the central, cavity of both R and T state Hb. The mechanism by which L35 reduces oxygen, affinity is discussed, in relation to spectroscopic studies of effector, binding.
+<StructureSection load='2d5x' size='340' side='right'caption='[[2d5x]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2d5x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D5X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D5X FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.45&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=L35:2-[4-({[(3,5-DICHLOROPHENYL)AMINO]CARBONYL}AMINO)PHENOXY]-2-METHYLPROPANOIC+ACID'>L35</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=2d5x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d5x OCA], [https://pdbe.org/2d5x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d5x RCSB], [https://www.ebi.ac.uk/pdbsum/2d5x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d5x ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HBA_HORSE HBA_HORSE] Involved in oxygen transport from the lung to the various peripheral tissues.
+== 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/d5/2d5x_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=2d5x ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-D5X is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus] with HEM, CMO and L35 as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D5X OCA].
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-R-state haemoglobin with low oxygen affinity: crystal structures of deoxy human and carbonmonoxy horse haemoglobin bound to the effector molecule L35., Yokoyama T, Neya S, Tsuneshige A, Yonetani T, Park SY, Tame JR, J Mol Biol. 2006 Feb 24;356(3):790-801. Epub 2005 Dec 21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16403522 16403522]
 [[Category: Equus caballus]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Neya, S.]]
+[[Category: Neya S]]
-[[Category: Park, S.Y.]]
+[[Category: Park SY]]
-[[Category: Tame, J.R.]]
+[[Category: Tame JR]]
-[[Category: Tsuneshige, A.]]
+[[Category: Tsuneshige A]]
-[[Category: Yokoyama, T.]]
+[[Category: Yokoyama T]]
-[[Category: Yonetani, T.]]
+[[Category: Yonetani T]]
-[[Category: CMO]]
-[[Category: HEM]]
-[[Category: L35]]
-[[Category: allosteric effector]]
-[[Category: crystal structure]]
-[[Category: hemoglobin]]
-[[Category: l35]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Thu Nov  8 13:29:13 2007''