4sdh: Difference between revisions

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-[[Image:4sdh.jpg|left|200px]]<br /><applet load="4sdh" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="4sdh, resolution 1.6&Aring;" />
-'''HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN'''<br />
-==Overview==
+==HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN==
-High-resolution crystal structures of the co-operative dimeric hemoglobin, from the blood clam Scapharca inaequivalvis have been determined in the, unliganded (deoxy) and carbon monoxide (CO) liganded states. The deoxy, structure has been refined at 1.6 A resolution to an R-factor of 0.158 and, the CO structure has been refined at 1.4 A resolution to an R-factor of, 0.159. These structures reveal details of the structural transitions, involved in co-operative ligand binding that involve only a minor rotation, of subunits but very striking tertiary changes at the interface. A small, number of residues in the F-helix appear to mediate co-operativity in this, simple hemoglobin. The oxygen affinity of each subunit appears to be, largely dictated by the disposition of phenylalanine 97, whose side-chain, packs in the heme pocket in the deoxy state but is extruded towards the, interface in the CO-liganded structure. Direct involvement of the, ligand-binding heme group is a novel feature of the subunit interface and, appears important for intersubunit communication. Ligation alters the, conformation of the heme propionate groups along with two interacting, residues from the symmetry-related subunit. These two residues, lysine 96, and asparagine 100, link the heme of one subunit with the F-helix of the, second subunit in such a way as to influence the ligand affinity of that, subunit. The interface is highly hydrated by well-ordered water molecules, that are likely to be important in the stabilization of the two, structures.
+<StructureSection load='4sdh' size='340' side='right'caption='[[4sdh]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4sdh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Anadara_inaequivalvis Anadara inaequivalvis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2sdh 2sdh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4SDH 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=4sdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4sdh OCA], [https://pdbe.org/4sdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4sdh RCSB], [https://www.ebi.ac.uk/pdbsum/4sdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4sdh ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLB1_ANAIN GLB1_ANAIN]
+== 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/sd/4sdh_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=4sdh ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-SDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca inaequivalvis] with <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 2SDH. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4SDH OCA].
+*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-High-resolution crystallographic analysis of a co-operative dimeric hemoglobin., Royer WE Jr, J Mol Biol. 1994 Jan 14;235(2):657-81. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8289287 8289287]
+[[Category: Anadara inaequivalvis]]
-[[Category: Scapharca inaequivalvis]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Royerjunior WE]]
-[[Category: Royerjunior, W.E.]]
-[[Category: HEM]]
-[[Category: oxygen transport]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:45:20 2008''