1f8d: Difference between revisions
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==Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid== | ==Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid== | ||
<StructureSection load='1f8d' size='340' side='right' caption='[[1f8d]], [[Resolution|resolution]] 1.40Å' scene=''> | <StructureSection load='1f8d' size='340' side='right' caption='[[1f8d]], [[Resolution|resolution]] 1.40Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1f8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/I75a5 I75a5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F8D FirstGlance]. <br> | <table><tr><td colspan='2'>[[1f8d]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/I75a5 I75a5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1F8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1F8D FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9AM:9-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>9AM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand= | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9AM:9-AMINO-2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC+ACID'>9AM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[7nn9|7nn9]], [[1f8b|1f8b]], [[1f8c|1f8c]], [[1f8e|1f8e]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[7nn9|7nn9]], [[1f8b|1f8b]], [[1f8c|1f8c]], [[1f8e|1f8e]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f8d OCA], [http://pdbe.org/1f8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f8d RCSB], [http://www.ebi.ac.uk/pdbsum/1f8d PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1f8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1f8d OCA], [http://pdbe.org/1f8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1f8d RCSB], [http://www.ebi.ac.uk/pdbsum/1f8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1f8d ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f8/1f8d_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f8/1f8d_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 1f8d" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 1f8d" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 12:24, 27 December 2017
Native Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic AcidNative Influenza Neuraminidase in Complex with 9-amino-2-deoxy-2,3-dehydro-N-neuraminic Acid
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed2,3-didehydro-2-deoxy-N:-acetylneuraminic acid (DANA) is a transition state analog inhibitor of influenza virus neuraminidase (NA). Replacement of the hydroxyl at the C9 position in DANA and 4-amino-DANA with an amine group, with the intention of taking advantage of an increased electrostatic interaction with a conserved acidic group in the active site to improve inhibitor binding, significantly reduces the inhibitor activity of both compounds. The three-dimensional X-ray structure of the complexes of these ligands and NA was obtained to 1.4 A resolution and showed that both ligands bind isosterically to DANA. Analysis of the geometry of the ammonium at the C4 position indicates that Glu119 may be neutral when these ligands bind. A computational analysis of the binding energies indicates that the substitution is successful in increasing the energy of interaction; however, the gains that are made are not sufficient to overcome the energy that is required to desolvate that part of the ligand that comes in contact with the protein. Analysis of inhibitor binding in influenza virus neuraminidase.,Smith BJ, Colman PM, Von Itzstein M, Danylec B, Varghese JN Protein Sci. 2001 Apr;10(4):689-96. PMID:11274459[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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