3gnc: Difference between revisions

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{{Seed}}
[[Image:3gnc.jpg|left|200px]]


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==Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with fragment 6421==
The line below this paragraph, containing "STRUCTURE_3gnc", creates the "Structure Box" on the page.
<StructureSection load='3gnc' size='340' side='right'caption='[[3gnc]], [[Resolution|resolution]] 2.15&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'>[[3gnc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GNC 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]] 2.15&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=QQQ:1-(1-METHYLETHYL)-1H-BENZIMIDAZOLE-2-SULFONIC+ACID'>QQQ</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
{{STRUCTURE_3gnc|  PDB=3gnc  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gnc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gnc OCA], [https://pdbe.org/3gnc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gnc RCSB], [https://www.ebi.ac.uk/pdbsum/3gnc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gnc ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q3JP94_BURP1 Q3JP94_BURP1]
== 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/gn/3gnc_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=3gnc ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.


===Crystal structure of Glutaryl-COA dehydrogenase from Burkholderia Pseudomallei with fragment 6421===
Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening.,Begley DW, Davies DR, Hartley RC, Hewitt SN, Rychel AL, Myler PJ, Van Voorhis WC, Staker BL, Stewart LJ Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Sep 1;67(Pt, 9):1060-9. Epub 2011 Aug 13. PMID:21904051<ref>PMID:21904051</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3gnc" style="background-color:#fffaf0;"></div>


==About this Structure==
==See Also==
3GNC is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GNC OCA].
*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
*[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Burkholderia pseudomallei 1710b]]
[[Category: Burkholderia pseudomallei 1710b]]
[[Category: Glutaryl-CoA dehydrogenase]]
[[Category: Large Structures]]
[[Category: SSGCID, Seattle Structural Genomics Center for Infectious Disease.]]
[[Category: Oxidoreductase]]
[[Category: Seattle structural genomics center for infectious disease]]
[[Category: Ssgcid]]
[[Category: Structural genomic]]
 
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Retrieved from "https://proteopedia.org/3gnc"