5mba: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(7 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:5mba.png|left|200px]]


<!--
==BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION==
The line below this paragraph, containing "STRUCTURE_5mba", creates the "Structure Box" on the page.
<StructureSection load='5mba' size='340' side='right'caption='[[5mba]], [[Resolution|resolution]] 1.90&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'>[[5mba]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aplysia_limacina Aplysia limacina]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MBA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MBA 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]] 1.9&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
{{STRUCTURE_5mba|  PDB=5mba  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5mba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mba OCA], [https://pdbe.org/5mba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mba RCSB], [https://www.ebi.ac.uk/pdbsum/5mba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mba ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/GLB_APLLI GLB_APLLI]
== 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/mb/5mba_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=5mba ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The binding mode of azide to the ferric form of Aplysia limacina myoglobin has been studied by X-ray crystallography. The three-dimensional structure of the complex has been refined at 1.9 A resolution to a crystallographic R-factor of 13.9%, including 126 ordered solvent molecules. Azide binds to the heme iron, at the sixth co-ordination position, and is oriented towards the outer part of the distal site crevice. This orientation is stabilized by an ionic interaction with the side-chain of Arg66 (E10) which, from an outer orientation in the 'aquo-met' ligand-free myoglobin, folds back towards the distal site in the presence of the anionic ligand. In the absence of a hydrogen bond donor residue at the distal E7 position in Aplysia limacina myoglobin, a different polar residue, Arg66 at the E10 topological position, has been selected by molecular evolution in order to grant ligand stabilization.


===BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION===
Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution.,Mattevi A, Gatti G, Coda A, Rizzi M, Ascenzi P, Brunori M, Bolognesi M J Mol Recognit. 1991 Feb;4(1):1-6. PMID:1931125<ref>PMID:1931125</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5mba" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_1931125}}, adds the Publication Abstract to the page
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 1931125 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_1931125}}
__TOC__
 
</StructureSection>
==About this Structure==
5MBA is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aplysia_limacina Aplysia limacina]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2mba 2mba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MBA OCA].
 
==Reference==
<ref group="xtra">PMID:1931125</ref><references group="xtra"/>
[[Category: Aplysia limacina]]
[[Category: Aplysia limacina]]
[[Category: Ascenzi, P.]]
[[Category: Large Structures]]
[[Category: Bolognesi, M.]]
[[Category: Ascenzi P]]
[[Category: Brunori, M.]]
[[Category: Bolognesi M]]
[[Category: Coda, A.]]
[[Category: Brunori M]]
[[Category: Gatti, G.]]
[[Category: Coda A]]
[[Category: Onesti, S.]]
[[Category: Gatti G]]
[[Category: Oxygen storage]]
[[Category: Onesti S]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:35:05 2009''
Retrieved from "https://proteopedia.org/5mba"