1dog: Difference between revisions

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-{{Seed}}
-[[Image:1dog.png|left|200px]]
-<!--
+==REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION==
-The line below this paragraph, containing "STRUCTURE_1dog", creates the "Structure Box" on the page.
+<StructureSection load='1dog' size='340' side='right'caption='[[1dog]], [[Resolution|resolution]] 2.30&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'>[[1dog]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. The February 2006 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DOG 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</scene></td></tr>
-{{STRUCTURE_1dog|  PDB=1dog  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dog OCA], [https://pdbe.org/1dog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dog RCSB], [https://www.ebi.ac.uk/pdbsum/1dog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dog ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/AMYG_ASPAW AMYG_ASPAW]
+== 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/do/1dog_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=1dog ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The three-dimensional structure of the complex of 1-deoxynojirimycin with glucoamylase II-(471) from Aspergillus awamori var. X100 has been determined to 2.4-A resolution. The model includes residues corresponding to residues 1-471 of glucoamylase I from Aspergillus niger, two molecules of bound 1-deoxynojirimycin and 605 sites for water molecules. The crystallographic R factor from refinement is 0.119, and the root-mean-squared deviation in bond distances is 0.012 A. The inhibitor complex confirms the location of the active site in the packing void of the alpha/alpha-barrel as proposed by Aleshin et al. [Aleshin, A., Golubev, A., Firsov, L., &amp; Honzatko, R. B. (1992) J. Biol. Chem. 267, 19291-19298]. One inhibitor molecule is associated with strong electron density and represents the principal site of interaction of 1-deoxynojirimycin with the enzyme. The other 1-deoxynojirimycin molecule is associated with weak electron density and therefore, probably represents a binding site of low affinity. Interactions of 1-deoxynojirimycin with the enzyme at its principal site involve Arg 45, Asp 55, Arg 305, and carbonyl 177. In addition, a water molecule (water 500) hydrogen bonds to Glu 400 and the 6-hydroxyl of 1-deoxynojirimycin and is at an approximate distance of 3.3 A from the "anomeric" carbon of the inhibitor. The structural arrangement of functional groups near the inhibitor molecule suggests that Glu 179 is a catalytic acid, Glu 400 a catalytic base, and water 500 the attacking nucleophile in the hydrolysis of maltooligosaccharides. The relevance of the X-ray work to proposed mechanisms of enzymatic hydrolysis of oligosaccharides is discussed.
-===REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION===
+Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from Aspergillus awamori var. X100 to 2.4-A resolution.,Harris EM, Aleshin AE, Firsov LM, Honzatko RB Biochemistry. 1993 Feb 16;32(6):1618-26. PMID:8431441<ref>PMID:8431441</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1dog" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_8431441}}, adds the Publication Abstract to the page
+*[[Alpha-glucosidase 3D structures|Alpha-glucosidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 8431441 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8431441}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DOG is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Aspergillus_awamori Aspergillus awamori]. The February 2006 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Alpha-amylase''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2006_2 10.2210/rcsb_pdb/mom_2006_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DOG OCA].
-==Reference==
-<ref group="xtra">PMID:8431441</ref><references group="xtra"/>
 [[Category: Alpha-amylase]]
 [[Category: Aspergillus awamori]]
-[[Category: Glucan 1,4-alpha-glucosidase]]
+[[Category: Large Structures]]
-[[Category: Aleshin, A.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Firsov, L.]]
+[[Category: Aleshin A]]
-[[Category: Harris, E.]]
+[[Category: Firsov L]]
-[[Category: Honzatko, R B.]]
+[[Category: Harris E]]
-[[Category: Hydrolase]]
+[[Category: Honzatko RB]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:11:26 2009''