1vah: Difference between revisions

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-[[Image:1vah.png|left|200px]]
-{{STRUCTURE_1vah|  PDB=1vah  |  SCENE=  }}
+==Crystal structure of the pig pancreatic-amylase complexed with r-nitrophenyl-a-D-maltoside==
+<StructureSection load='1vah' size='340' side='right'caption='[[1vah]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vah]] is a 1 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=1VAH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VAH FirstGlance]. <br>
+</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>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NPO:P-NITROPHENOL'>NPO</scene></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=1vah FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vah OCA], [https://pdbe.org/1vah PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vah RCSB], [https://www.ebi.ac.uk/pdbsum/1vah PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vah ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYP_PIG AMYP_PIG]
+== 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/va/1vah_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=1vah ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray structure analysis of a crystal of pig pancreatic alpha-amylase soaked with a rho-nitrophenyl-alpha-D-maltoside (pNPG2) substrate showed a pattern of electron density corresponding to the binding of a rho-nitrophenol unit at subsite -2 of the active site. Binding of the product to subsite -2 after hydrolysis of the pNPG2 molecules, may explain the low catalytic efficiency of the hydrolysis of pNPG2 by PPA. Except a small movement of the segment from residues 304-305 the typical conformational changes of the "flexible loop" (303-309), that constitutes the surface edge of the substrate binding cleft, were not observed in the present complex structure. This result supports the hypothesis that significant movement of the loop may depend on aglycone site being filled (Payan and Qian, J. Protein Chen. 22: 275, 2003). Structural analyses have shown that pancreatic alpha-amylases undergo an induced conformational change of the catalytic residue Asp300 upon substrate binding; in the present complex the catalytic residue is observed in its unliganded orientation. The results suggest that the induced reorientation is likely due to the presence of a sugar unit at subsite -1 and not linked to the closure of the flexible surface loop. The crystal structure was refined at 2.4 A resolution to an R factor of 17.55% (Rfree factor of 23.32%).
-===Crystal structure of the pig pancreatic-amylase complexed with r-nitrophenyl-a-D-maltoside===
+Crystal structure of the pig pancreatic alpha-amylase complexed with rho-nitrophenyl-alpha-D-maltoside-flexibility in the active site.,Zhuo H, Payan F, Qian M Protein J. 2004 Aug;23(6):379-87. PMID:15517985<ref>PMID:15517985</ref>
-{{ABSTRACT_PUBMED_15517985}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 1vah" style="background-color:#fffaf0;"></div>
-[[1vah]] is a 1 chain structure of [[Alpha-Amylase]] with 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=1VAH OCA].
 ==See Also==
-*[[Alpha-Amylase|Alpha-Amylase]]
+*[[Amylase 3D structures|Amylase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:015517985</ref><ref group="xtra">PMID:009385631</ref><ref group="xtra">PMID:012962327</ref><references group="xtra"/>
+__TOC__
-[[Category: Alpha-amylase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Sus scrofa]]
-[[Category: Payan, F.]]
+[[Category: Payan F]]
-[[Category: Qian, M.]]
+[[Category: Qian M]]
-[[Category: Zhuo, H.]]
+[[Category: Zhuo H]]
-[[Category: Beta-alpha-barrel]]
-[[Category: Hydrolase]]