4sdh: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(9 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:4sdh.jpg|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_4sdh", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_4sdh|  PDB=4sdh  |  SCENE=  }}
'''HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN'''


==HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN==
<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]. 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/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=4sdh ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
High-resolution crystallographic analysis of a co-operative dimeric hemoglobin.,Royer WE Jr J Mol Biol. 1994 Jan 14;235(2):657-81. PMID:8289287<ref>PMID:8289287</ref>
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.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
4SDH is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Scapharca_inaequivalvis Scapharca 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].
</div>
<div class="pdbe-citations 4sdh" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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://www.ncbi.nlm.nih.gov/pubmed/8289287 8289287]
*[[Hemoglobin 3D structures|Hemoglobin 3D structures]]
[[Category: Scapharca inaequivalvis]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Royerjunior, W E.]]
__TOC__
[[Category: Oxygen transport]]
</StructureSection>
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 22:29:22 2008''
[[Category: Anadara inaequivalvis]]
[[Category: Large Structures]]
[[Category: Royerjunior WE]]

Latest revision as of 11:48, 13 August 2026

HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN

4sdh, resolution 1.60Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=4sdh&oldid=4478979"