This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


2ogj

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (00:18, 28 December 2023) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2ogj.gif|left|200px]]
 
-
{{Structure
+
==Crystal structure of a dihydroorotase==
-
|PDB= 2ogj |SIZE=350|CAPTION= <scene name='initialview01'>2ogj</scene>, resolution 2.62&Aring;
+
<StructureSection load='2ogj' size='340' side='right'caption='[[2ogj]], [[Resolution|resolution]] 2.62&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=LCX:CARBOXYLATED+LYSINE'>LCX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+
<table><tr><td colspan='2'>[[2ogj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_fabrum_str._C58 Agrobacterium fabrum str. C58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGJ FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.62&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-
|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01307 Met_dep_hydrolase_B], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=COG3964 COG3964]</span>
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ogj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ogj OCA], [https://pdbe.org/2ogj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ogj RCSB], [https://www.ebi.ac.uk/pdbsum/2ogj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ogj ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2ogj TOPSAN]</span></td></tr>
-
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ogj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ogj OCA], [http://www.ebi.ac.uk/pdbsum/2ogj PDBsum], [http://www.fli-leibniz.de/cgi-bin/ImgLib.pl?CODE=1kfv JenaLib], [http://www.rcsb.org/pdb/explore.do?structureId=2ogj RCSB]</span>
+
</table>
-
}}
+
== Function ==
 +
[https://www.uniprot.org/uniprot/DEACT_AGRFC DEACT_AGRFC] Esterase that catalyzes the deacetylation of acetyl-(R)-mandelate (in vitro). Can also hydrolyze acetyl glycolate, but with lower efficiency. Has very low N-acetyl-D-amino acid deacetylase activity with N-acetyl-D-serine and N-acetyl-D-threonine (in vitro). Theoretical substrate docking studies suggest that other N-acetylated amino acids may optimally occupy the active site and may in fact be the physiological substrates.<ref>PMID:23214420</ref>
 +
== 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/og/2ogj_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=2ogj ConSurf].
 +
<div style="clear:both"></div>
-
'''Crystal structure of a dihydroorotase'''
+
==See Also==
-
 
+
*[[Dihydroorotase 3D structures|Dihydroorotase 3D structures]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
2OGJ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGJ OCA].
+
__TOC__
-
[[Category: Agrobacterium tumefaciens]]
+
</StructureSection>
-
[[Category: Single protein]]
+
[[Category: Agrobacterium fabrum str. C58]]
-
[[Category: Burley, S K.]]
+
[[Category: Large Structures]]
-
[[Category: Kumaran, D.]]
+
[[Category: Burley SK]]
-
[[Category: NYSGXRC, New York Structural GenomiX Research Consortium.]]
+
[[Category: Kumaran D]]
-
[[Category: Sugadev, R.]]
+
[[Category: Sugadev R]]
-
[[Category: Swaminathan, S.]]
+
[[Category: Swaminathan S]]
-
[[Category: 9244b]]
+
-
[[Category: amido hydrolase]]
+
-
[[Category: binuclear zinc]]
+
-
[[Category: imidazole complex]]
+
-
[[Category: new york structural genomix research consortium]]
+
-
[[Category: nysgxrc]]
+
-
[[Category: protein structure initiative]]
+
-
[[Category: psi-2]]
+
-
[[Category: structural genomic]]
+
-
[[Category: tim barrel]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 26 06:36:38 2008''
+

Current revision

Crystal structure of a dihydroorotase

PDB ID 2ogj

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ogj"
Personal tools