5mba

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[[Image:5mba.gif|left|200px]]
 
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{{Structure
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==BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION==
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|PDB= 5mba |SIZE=350|CAPTION= <scene name='initialview01'>5mba</scene>, resolution 1.9&Aring;
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<StructureSection load='5mba' size='340' side='right'caption='[[5mba]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <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>
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<table><tr><td colspan='2'>[[5mba]] is a 1 chain structure with sequence from [https://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]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MBA FirstGlance]. <br>
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|ACTIVITY=
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</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>
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|GENE=
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<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>
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|DOMAIN=
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<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>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5mba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mba OCA], [http://www.ebi.ac.uk/pdbsum/5mba PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=5mba RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/GLB_APLLI GLB_APLLI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mb/5mba_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION'''
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5mba" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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.
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*[[Myoglobin 3D structures|Myoglobin 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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5MBA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Aplysia_limacina Aplysia limacina]. This structure supersedes the now removed PDB entry 2MBA. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MBA OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/1931125 1931125]
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[[Category: Aplysia limacina]]
[[Category: Aplysia limacina]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Ascenzi, P.]]
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[[Category: Ascenzi P]]
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[[Category: Bolognesi, M.]]
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[[Category: Bolognesi M]]
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[[Category: Brunori, M.]]
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[[Category: Brunori M]]
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[[Category: Coda, A.]]
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[[Category: Coda A]]
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[[Category: Gatti, G.]]
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[[Category: Gatti G]]
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[[Category: Onesti, S.]]
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[[Category: Onesti S]]
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[[Category: oxygen storage]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:41:51 2008''
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Current revision

BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION

PDB ID 5mba

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