2buc: Difference between revisions

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-{{Seed}}
-[[Image:2buc.png|left|200px]]
-<!--
+==Crystal Structure Of Porcine Dipeptidyl Peptidase IV (CD26) in Complex with a Tetrahydroisoquinoline Inhibitor==
-The line below this paragraph, containing "STRUCTURE_2buc", creates the "Structure Box" on the page.
+<StructureSection load='2buc' size='340' side='right'caption='[[2buc]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2buc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BUC FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=008:(S)-2-[(R)-3-AMINO-4-(2-FLUORO-PHENYL)-BUTYRYL]-1,2,3,4-TETRAHYDRO-ISOQUINOLINE-3-CARBOXYLIC+ACID+AMIDE'>008</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2buc|  PDB=2buc  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2buc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2buc OCA], [https://pdbe.org/2buc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2buc RCSB], [https://www.ebi.ac.uk/pdbsum/2buc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2buc ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPP4_PIG DPP4_PIG] Cell surface glycoprotein receptor involved in the costimulatory signal essential for T-cell receptor (TCR)-mediated T-cell activation. Acts as a positive regulator of T-cell coactivation, by binding at least ADA, CAV1, IGF2R, and PTPRC. Its binding to CAV1 and CARD11 induces T-cell proliferation and NF-kappa-B activation in a T-cell receptor/CD3-dependent manner. Its interaction with ADA also regulates lymphocyte-epithelial cell adhesion. In association with FAP is involved in the pericellular proteolysis of the extracellular matrix (ECM), the migration and invasion of endothelial cells into the ECM. May be involved in the promotion of lymphatic endothelial cells adhesion, migration and tube formation. When overexpressed, enhanced cell proliferation, a process inhibited by GPC3. Acts also as a serine exopeptidase with a dipeptidyl peptidase activity that regulates various physiological processes by cleaving peptides in the circulation, including many chemokines, mitogenic growth factors, neuropeptides and peptide hormones (By similarity). Removes N-terminal dipeptides sequentially from polypeptides having unsubstituted N-termini provided that the penultimate residue is proline.<ref>PMID:14719797</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/bu/2buc_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2buc ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The co-crystal structure of beta-phenethylamine fragment inhibitor 5 bound to DPP-IV revealed that the phenyl ring occupied the proline pocket of the enzyme. This finding provided the basis for a general hypothesis of a reverse binding mode for beta-phenethylamine-based DPP-IV inhibitors. Novel inhibitor design concepts that obviate substrate-like structure-activity relationships (SAR) were thereby enabled, and novel, potent inhibitors were discovered.
-===CRYSTAL STRUCTURE OF PORCINE DIPEPTIDYL PEPTIDASE IV (CD26) IN COMPLEX WITH A TETRAHYDROISOQUINOLINE INHIBITOR===
+The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors.,Nordhoff S, Cerezo-Galvez S, Feurer A, Hill O, Matassa VG, Metz G, Rummey C, Thiemann M, Edwards PJ Bioorg Med Chem Lett. 2006 Mar 15;16(6):1744-8. Epub 2006 Jan 11. PMID:16376544<ref>PMID:16376544</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2buc" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16376544}}, adds the Publication Abstract to the page
+*[[Dipeptidyl peptidase 3D structures|Dipeptidyl peptidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16376544 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16376544}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BUC is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BUC OCA].
-==Reference==
-The reversed binding of beta-phenethylamine inhibitors of DPP-IV: X-ray structures and properties of novel fragment and elaborated inhibitors., Nordhoff S, Cerezo-Galvez S, Feurer A, Hill O, Matassa VG, Metz G, Rummey C, Thiemann M, Edwards PJ, Bioorg Med Chem Lett. 2006 Mar 15;16(6):1744-8. Epub 2006 Jan 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16376544 16376544]
-[[Category: Dipeptidyl-peptidase IV]]
-[[Category: Single protein]]
 [[Category: Sus scrofa]]
-[[Category: Cerezo-Galvez, S.]]
+[[Category: Cerezo-Galvez S]]
-[[Category: Edwards, P J.]]
+[[Category: Edwards PJ]]
-[[Category: Feurer, A.]]
+[[Category: Feurer A]]
-[[Category: Hill, O.]]
+[[Category: Hill O]]
-[[Category: Matassa, V G.]]
+[[Category: Matassa VG]]
-[[Category: Metz, G.]]
+[[Category: Metz G]]
-[[Category: Nordhoff, S.]]
+[[Category: Nordhoff S]]
-[[Category: Rummey, C.]]
+[[Category: Rummey C]]
-[[Category: Thiemann, M.]]
+[[Category: Thiemann M]]
-[[Category: Aminopeptidase]]
-[[Category: Complex]]
-[[Category: Diabetes mellitus]]
-[[Category: Dpp-iv]]
-[[Category: Drug design]]
-[[Category: Glycoprotein]]
-[[Category: Hydrolase]]
-[[Category: Protease]]
-[[Category: Serine protease]]
-[[Category: Signal-anchor]]
-[[Category: Transmembrane]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:56:28 2008''