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4tim

From Proteopedia

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[[Image:4tim.jpg|left|200px]]<br /><applet load="4tim" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="4tim, resolution 2.4&Aring;" />
 
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'''CRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: A CRITICAL ASSESSMENT OF THE PREDICTED AND OBSERVED STRUCTURES OF THE COMPLEX WITH 2-PHOSPHOGLYCERATE'''<br />
 
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==Overview==
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==CRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: A CRITICAL ASSESSMENT OF THE PREDICTED AND OBSERVED STRUCTURES OF THE COMPLEX WITH 2-PHOSPHOGLYCERATE==
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In the continuation of a project aimed at the rational design of drugs against diseases caused by trypanosomes, the crystal structure of trypanosomal triosephosphate isomerase in complex with the active site inhibitor 2-phosphoglycerate has been determined. Two alternative modeling protocols have been attempted to predict the mode of binding of this ligand. In the first protocol, certain key interactions were restrained in the modeling procedure. In the second protocol, a full search of ligand conformational space was performed. In both cases the protein scaffold was kept static. Both protocols produced models which were reasonably close to the observed structure (rms difference less than 2.0 A). Nevertheless, some essential features were missed by each of the protocols. The crystallographic structure of the 2-PGA TIM complex shows that the ligand binds fully within the active site of TIM, with partners for all but one of the ligand's strongly hydrogen bonding groups. Several of the interactions between the ligand and the active site of TIM are seen to be common to all of the complexes so far structurally characterized between trypanosomal triosephosphate isomerase and competitive inhibitors. Such key interactions appear to be the best guide in the prediction of the binding mode of a new inhibitor.
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<StructureSection load='4tim' size='340' side='right'caption='[[4tim]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4tim]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TIM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TIM FirstGlance]. <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]] 2.4&#8491;</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=2PG:2-PHOSPHOGLYCERIC+ACID'>2PG</scene></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=4tim FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tim OCA], [https://pdbe.org/4tim PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tim RCSB], [https://www.ebi.ac.uk/pdbsum/4tim PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tim ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/TPIS_TRYBB TPIS_TRYBB]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ti/4tim_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</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/main_output.php?pdb_ID=4tim ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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4TIM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Trypanosoma_brucei_brucei Trypanosoma brucei brucei] with <scene name='pdbligand=2PG:'>2PG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Triose-phosphate_isomerase Triose-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.1 5.3.1.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TIM OCA].
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*[[Triose phosphate isomerase 3D structures|Triose phosphate isomerase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Crystallographic and molecular modeling studies on trypanosomal triosephosphate isomerase: a critical assessment of the predicted and observed structures of the complex with 2-phosphoglycerate., Noble ME, Verlinde CL, Groendijk H, Kalk KH, Wierenga RK, Hol WG, J Med Chem. 1991 Sep;34(9):2709-18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1895291 1895291]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Triose-phosphate isomerase]]
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[[Category: Trypanosoma brucei brucei]]
[[Category: Trypanosoma brucei brucei]]
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[[Category: Hol, W G.J.]]
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[[Category: Hol WGJ]]
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[[Category: Nobel, M E.M.]]
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[[Category: Nobel MEM]]
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[[Category: Wierenga, R K.]]
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[[Category: Wierenga RK]]
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[[Category: 2PG]]
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[[Category: isomerase(intramolecular oxidoreductase)]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:14:24 2008''
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Current revision

CRYSTALLOGRAPHIC AND MOLECULAR MODELING STUDIES ON TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE: A CRITICAL ASSESSMENT OF THE PREDICTED AND OBSERVED STRUCTURES OF THE COMPLEX WITH 2-PHOSPHOGLYCERATE

PDB ID 4tim

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