5cb4: Difference between revisions

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<StructureSection load='5cb4' size='340' side='right'caption='[[5cb4]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
<StructureSection load='5cb4' size='340' side='right'caption='[[5cb4]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5cb4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Buffalo_rat Buffalo rat], [http://en.wikipedia.org/wiki/Chick Chick] and [http://en.wikipedia.org/wiki/Sus_barbatus Sus barbatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5CB4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[5cb4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus], [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus] and [https://en.wikipedia.org/wiki/Sus_barbatus Sus barbatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5CB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5CB4 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TIV:(3R,4R)-3-(5,6-DIHYDRO-4H-PYRROLO[3,2,1-IJ]QUINOLIN-1-YL)-4-(1H-INDOL-3-YL)PYRROLIDINE-2,5-DIONE'>TIV</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]] 2.193&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5c8y|5c8y]], [[5ca0|5ca0]], [[5ca1|5ca1]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACP:PHOSPHOMETHYLPHOSPHONIC+ACID+ADENYLATE+ESTER'>ACP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TIV:(3R,4R)-3-(5,6-DIHYDRO-4H-PYRROLO[3,2,1-IJ]QUINOLIN-1-YL)-4-(1H-INDOL-3-YL)PYRROLIDINE-2,5-DIONE'>TIV</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Stmn4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10116 Buffalo rat]), TTL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</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=5cb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cb4 OCA], [https://pdbe.org/5cb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5cb4 RCSB], [https://www.ebi.ac.uk/pdbsum/5cb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5cb4 ProSAT]</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=5cb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5cb4 OCA], [http://pdbe.org/5cb4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5cb4 RCSB], [http://www.ebi.ac.uk/pdbsum/5cb4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5cb4 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://www.uniprot.org/uniprot/STMN4_RAT STMN4_RAT]] Exhibits microtubule-destabilizing activity.<ref>PMID:15039434</ref> <ref>PMID:12111843</ref> <ref>PMID:15014504</ref> 
[https://www.uniprot.org/uniprot/A0A0R4I993_SUSBA A0A0R4I993_SUSBA] Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain.[RuleBase:RU000352][SAAS:SAAS00824325]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Microtubules are dynamic assemblies of alphabeta-tubulin heterodimers and have been recognized as highly attractive targets for cancer chemotherapy. A broad range of agents bind to tubulin and interfere with microtubule assembly. Despite having a long history of characterization, colchicine binding site inhibitors (CBSIs) have not yet reached the commercial phase as anti-cancer drugs to date. We determined the structures of tubulin complexed with a set of structurally diverse CBSIs (lexibulin, nocodazole, plinabulin and tivantinib), among which nocodazole and tivantinib are both binary-function inhibitors targeting cancer-related kinases and microtubules simultaneously. High resolution structures revealed the detailed interactions between these ligands and tubulin. Our results showed that the binding modes of the CBSIs were different from previous docking models, highlighting the importance of crystal structure information in structure-based drug design. A real structure-based pharmacophore was proposed to rationalize key common interactions of the CBSIs at the colchicine domain. Our studies provide a solid structural basis for developing new anti-cancer agents for the colchicine binding site. DATABASE: The atomic coordinates and structure factors for tubulin complexed with lexibulin, nocodazole, plinabulin and tivantinib have been deposited in the Protein Data Bank under accession codes 5CA0, 5CA1, 5C8Y and 5CB4, respectively.
 
Structures of a diverse set of colchicine binding site inhibitors in complex with tubulin provide a rationale for drug discovery.,Wang Y, Zhang H, Gigant B, Yu Y, Wu Y, Chen X, Lai Q, Yang Z, Chen Q, Yang J FEBS J. 2016 Jan;283(1):102-11. doi: 10.1111/febs.13555. Epub 2015 Nov 4. PMID:26462166<ref>PMID:26462166</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5cb4" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Stathmin-4 3D structures|Stathmin-4 3D structures]]
*[[Stathmin-4 3D structures|Stathmin-4 3D structures]]
*[[Tubulin 3D Structures|Tubulin 3D Structures]]
*[[Tubulin 3D Structures|Tubulin 3D Structures]]
*[[Tubulin tyrosine ligase|Tubulin tyrosine ligase]]
*[[Tubulin tyrosine ligase 3D structures|Tubulin tyrosine ligase 3D structures]]
*[[User:Alisa Cario|User:Alisa Cario]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Buffalo rat]]
[[Category: Gallus gallus]]
[[Category: Chick]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Rattus norvegicus]]
[[Category: Sus barbatus]]
[[Category: Sus barbatus]]
[[Category: Chen, Q]]
[[Category: Chen Q]]
[[Category: Wang, Y]]
[[Category: Wang Y]]
[[Category: Yang, J]]
[[Category: Yang J]]
[[Category: Yu, Y]]
[[Category: Yu Y]]
[[Category: Complex]]
[[Category: Inhibitor]]
[[Category: Structural protein]]
[[Category: Tubulin]]

Latest revision as of 12:08, 20 March 2024

Crystal structure of T2R-TTL-Tivantinib complexCrystal structure of T2R-TTL-Tivantinib complex

Structural highlights

5cb4 is a 6 chain structure with sequence from Gallus gallus, Rattus norvegicus and Sus barbatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.193Å
Ligands:, , , , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A0R4I993_SUSBA Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain.[RuleBase:RU000352][SAAS:SAAS00824325]

See Also

5cb4, resolution 2.19Å

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OCA
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