2yxx: Difference between revisions

From Proteopedia
Jump to navigationJump to search
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
New page: left|200px<br /><applet load="2yxx" size="350" color="white" frame="true" align="right" spinBox="true" caption="2yxx, resolution 1.70Å" /> '''Crystal structure an...
 
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,332,843 edits
No edit summary
 
(14 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2yxx.gif|left|200px]]<br /><applet load="2yxx" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2yxx, resolution 1.70&Aring;" />
'''Crystal structure analysis of Diaminopimelate decarboxylate (lysA)'''<br />


==About this Structure==
==Crystal structure analysis of Diaminopimelate decarboxylate (lysA)==
2YXX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with <scene name='pdbligand=PLP:'>PLP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Diaminopimelate_decarboxylase Diaminopimelate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.20 4.1.1.20] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXX OCA].
<StructureSection load='2yxx' size='340' side='right'caption='[[2yxx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
[[Category: Diaminopimelate decarboxylase]]
== Structural highlights ==
[[Category: Single protein]]
<table><tr><td colspan='2'>[[2yxx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YXX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YXX FirstGlance]. <br>
[[Category: Thermotoga maritima]]
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
[[Category: Bessho, Y.]]
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
[[Category: Nakamura, Y.]]
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yxx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yxx OCA], [https://pdbe.org/2yxx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yxx RCSB], [https://www.ebi.ac.uk/pdbsum/2yxx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yxx ProSAT], [https://www.topsan.org/Proteins/RSGI/2yxx TOPSAN]</span></td></tr>
[[Category: Padmanabhan, B.]]
</table>
[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
== Function ==
[[Category: Yokoyama, S.]]
[https://www.uniprot.org/uniprot/DCDA_THEMA DCDA_THEMA] Specifically catalyzes the decarboxylation of meso-diaminopimelate (meso-DAP) to L-lysine (By similarity).[HAMAP-Rule:MF_02120]
[[Category: PLP]]
== Evolutionary Conservation ==
[[Category: lyase]]
[[Image:Consurf_key_small.gif|200px|right]]
[[Category: national project on protein structural and functional analyses]]
Check<jmol>
[[Category: nppsfa]]
  <jmolCheckbox>
[[Category: riken structural genomics/proteomics initiative]]
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yxx_consurf.spt"</scriptWhenChecked>
[[Category: rsgi]]
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
[[Category: structural genomics]]
    <text>to colour the structure by Evolutionary Conservation</text>
[[Category: tim beta/alpha barrel fold]]
  </jmolCheckbox>
[[Category: tm1517]]
</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=2yxx ConSurf].
 
<div style="clear:both"></div>
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 12:39:30 2008''
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermotoga maritima MSB8]]
[[Category: Bessho Y]]
[[Category: Nakamura Y]]
[[Category: Padmanabhan B]]
[[Category: Yokoyama S]]
Retrieved from "https://proteopedia.org/2yxx"