3d6b: 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
 
Line 3: Line 3:
<StructureSection load='3d6b' size='340' side='right'caption='[[3d6b]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
<StructureSection load='3d6b' size='340' side='right'caption='[[3d6b]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3d6b]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D6B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3d6b]] 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=3D6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D6B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=54D:METHYL+THIOPHENE-2-CARBOXYLATE'>54D</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.21&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BURPS1710b_3237 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=54D:METHYL+THIOPHENE-2-CARBOXYLATE'>54D</scene></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glutaryl-CoA_dehydrogenase_(ETF) Glutaryl-CoA dehydrogenase (ETF)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.8.6 1.3.8.6] </span></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=3d6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d6b OCA], [https://pdbe.org/3d6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d6b RCSB], [https://www.ebi.ac.uk/pdbsum/3d6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d6b ProSAT], [https://www.topsan.org/Proteins/SSGCID/3d6b TOPSAN]</span></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=3d6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d6b OCA], [https://pdbe.org/3d6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d6b RCSB], [https://www.ebi.ac.uk/pdbsum/3d6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d6b ProSAT], [https://www.topsan.org/Proteins/SSGCID/3d6b TOPSAN]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q3JP94_BURP1 Q3JP94_BURP1]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Line 19: Line 20:
</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=3d6b ConSurf].
</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=3d6b ConSurf].
<div style="clear:both"></div>
<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.
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 3d6b" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
*[[Acyl-CoA dehydrogenase 3D structures|Acyl-CoA dehydrogenase 3D structures]]
*[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]]
*[[Glutaryl-CoA dehydrogenase|Glutaryl-CoA dehydrogenase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Burp1]]
[[Category: Burkholderia pseudomallei 1710b]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Structural genomic]]
[[Category: Burkholderia]]
[[Category: Dehydrogenase]]
[[Category: Fad]]
[[Category: Flavoprotein]]
[[Category: Glutaryl-coa]]
[[Category: Oxidoreductase]]
[[Category: Pseudomallei]]
[[Category: Ssgcid]]
Retrieved from "https://proteopedia.org/3d6b"