2q4x

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==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990==
==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990==
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<StructureSection load='2q4x' size='340' side='right' caption='[[2q4x]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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<StructureSection load='2q4x' size='340' side='right'caption='[[2q4x]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[2q4x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4X OCA]. <br>
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<table><tr><td colspan='2'>[[2q4x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q4X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q4X FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HMH:4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE'>HMH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;, 8 models</td></tr>
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<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=HMH:4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE'>HMH</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2f2g|2f2g]]</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4x OCA], [https://pdbe.org/2q4x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q4x RCSB], [https://www.ebi.ac.uk/pdbsum/2q4x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q4x ProSAT]</span></td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g16990, K14A17_11, K14A17.22 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</td></tr>
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</table>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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== Function ==
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q4x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q4x OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q4x RCSB], [http://www.ebi.ac.uk/pdbsum/2q4x PDBsum]</span></td></tr>
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[https://www.uniprot.org/uniprot/TENAE_ARATH TENAE_ARATH] Involved in thiamine salvage by hydrolyzing the thiamine breakdown product 4-amino-5-aminomethyl-2-methylpyrimidine (amino-HMP) to 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) (PubMed:25014715). Has a high formylamino-HMP amidohydrolase activity (PubMed:25014715). No activity with other thiamine degradation products such as thiamine mono- or diphosphate, oxothiamine, oxythiamine, thiamine disulfide, desthiothiamine or thiochrome as substrates (PubMed:25014715). Does not display thiaminase II activity, as it is unable to hydrolyze thiamine (PubMed:25014715). Is able to carry out two successive steps in the salvage of thiamine breakdown product, whereas two separate enzymes are required in Bacillus species (Probable). May also serve a damage pre-emption function by hydrolyzing products that would otherwise do harm (Probable).<ref>PMID:25014715</ref> <ref>PMID:25014715</ref>
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<table>
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== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4x_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q4/2q4x_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmolCheckbox>
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</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/chain_selection.php?pdb_ID=2ata ConSurf].
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</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=2q4x ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
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Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>
Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744<ref>PMID:17850744</ref>
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 2q4x" style="background-color:#fffaf0;"></div>
== References ==
== References ==
<references/>
<references/>
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</StructureSection>
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Arabidopsis thaliana]]
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[[Category: CESG, Center for Eukaryotic Structural Genomics.]]
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[[Category: Large Structures]]
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[[Category: Kondrashov, D A.]]
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[[Category: Kondrashov DA]]
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[[Category: Levin, E J.]]
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[[Category: Levin EJ]]
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[[Category: Phillips, G N.]]
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[[Category: Phillips Jr GN]]
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[[Category: Wesenberg, G E.]]
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[[Category: Wesenberg GE]]
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[[Category: At3g16990]]
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[[Category: Center for eukaryotic structural genomic]]
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[[Category: Cesg]]
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[[Category: Ensemble refinement]]
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[[Category: Plant protein]]
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[[Category: Protein structure initiative]]
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[[Category: Psi]]
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[[Category: Refinement methodology development]]
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[[Category: Structural genomic]]
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[[Category: Tena/thi-4/pqqc family]]
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[[Category: Tena_thi-4 domain]]
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Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g16990

PDB ID 2q4x

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