2f1a: Difference between revisions

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 ==GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (2R,3R,4S)-2-({[(1S)-2-hydroxy-1-phenylethyl]amino}methyl)pyrrolidine-3,4-diol==
-<StructureSection load='2f1a' size='340' side='right' caption='[[2f1a]], [[Resolution|resolution]] 1.45&Aring;' scene=''>
+<StructureSection load='2f1a' size='340' side='right'caption='[[2f1a]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2f1a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2F1A FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F1A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GB2:(2R,3R,4S)-2-({[(1S)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)PYRROLIDINE-3,4-DIOL'>GB2</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</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=2f1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f1a OCA], [https://pdbe.org/2f1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f1a RCSB], [https://www.ebi.ac.uk/pdbsum/2f1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f1a ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hty|1hty]], [[1hww|1hww]], [[1hxk|1hxk]], [[1ps2|1ps2]], [[1qwn|1qwn]], [[1qx1|1qx1]], [[1r33|1r33]], [[1r34|1r34]], [[1tqs|1tqs]], [[1tqt|1tqt]], [[1tqu|1tqu]], [[1tqw|1tqw]], [[2alw|2alw]], [[2f18|2f18]], [[2f1b|2f1b]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alpha-Man-II, GmII ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Mannosyl-oligosaccharide_1,3-1,6-alpha-mannosidase Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.114 3.2.1.114] </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=2f1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f1a OCA], [http://pdbe.org/2f1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2f1a RCSB], [http://www.ebi.ac.uk/pdbsum/2f1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2f1a ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
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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=2f1a ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.
-Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.,Englebienne P, Fiaux H, Kuntz DA, Corbeil CR, Gerber-Lemaire S, Rose DR, Moitessier N Proteins. 2007 Oct 1;69(1):160-76. PMID:17557336<ref>PMID:17557336</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2f1a" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Mannosidase|Mannosidase]]
+*[[Mannosidase 3D structures|Mannosidase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Drome]]
+[[Category: Large Structures]]
-[[Category: Mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase]]
+[[Category: Kuntz DA]]
-[[Category: Kuntz, D A]]
+[[Category: Rose DR]]
-[[Category: Rose, D R]]
-[[Category: Glycosyl hydrolase family 38]]
-[[Category: Hydrolase]]