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.


1ra0

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:02, 23 August 2023) (edit) (undo)
 
(3 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Bacterial cytosine deaminase D314G mutant bound to 5-fluoro-4-(S)-hydroxy-3,4-dihydropyrimidine.==
==Bacterial cytosine deaminase D314G mutant bound to 5-fluoro-4-(S)-hydroxy-3,4-dihydropyrimidine.==
-
<StructureSection load='1ra0' size='340' side='right' caption='[[1ra0]], [[Resolution|resolution]] 1.12&Aring;' scene=''>
+
<StructureSection load='1ra0' size='340' side='right'caption='[[1ra0]], [[Resolution|resolution]] 1.12&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[1ra0]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RA0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RA0 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[1ra0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RA0 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FPY:(4S)-5-FLUORO-4-HYDROXY-3,4-DIHYDROPYRIMIDIN-2(1H)-ONE'>FPY</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]] 1.12&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1k7o|1k7o]], [[1r9x|1r9x]], [[1r9y|1r9y]], [[1r9z|1r9z]], [[1ra5|1ra5]], [[1rak|1rak]], [[1rb7|1rb7]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FPY:(4S)-5-FLUORO-4-HYDROXY-3,4-DIHYDROPYRIMIDIN-2(1H)-ONE'>FPY</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CODA, B0337 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1ra0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ra0 OCA], [https://pdbe.org/1ra0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ra0 RCSB], [https://www.ebi.ac.uk/pdbsum/1ra0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ra0 ProSAT]</span></td></tr>
-
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytosine_deaminase Cytosine deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.4.1 3.5.4.1] </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=1ra0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ra0 OCA], [http://pdbe.org/1ra0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ra0 RCSB], [http://www.ebi.ac.uk/pdbsum/1ra0 PDBsum]</span></td></tr>
+
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CODA_ECOLI CODA_ECOLI]
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
-
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ra/1ra0_consurf.spt"</scriptWhenChecked>
+
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ra/1ra0_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>
Line 30: Line 31:
==See Also==
==See Also==
-
*[[Deaminase|Deaminase]]
+
*[[Deaminase 3D structures|Deaminase 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Bacillus coli migula 1895]]
+
[[Category: Escherichia coli]]
-
[[Category: Cytosine deaminase]]
+
[[Category: Large Structures]]
-
[[Category: Black, M E]]
+
[[Category: Black ME]]
-
[[Category: Ireton, G C]]
+
[[Category: Ireton GC]]
-
[[Category: Mahan, S D]]
+
[[Category: Mahan SD]]
-
[[Category: Stoddard, B L]]
+
[[Category: Stoddard BL]]
-
[[Category: Alpha-beta barrel]]
+
-
[[Category: Conformational change]]
+
-
[[Category: D314g mutant]]
+
-
[[Category: Hexamer]]
+
-
[[Category: Hydrolase]]
+

Current revision

Bacterial cytosine deaminase D314G mutant bound to 5-fluoro-4-(S)-hydroxy-3,4-dihydropyrimidine.

PDB ID 1ra0

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools