1gdu: Difference between revisions

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-[[Image:1gdu.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1gdu", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_1gdu|  PDB=1gdu  |  SCENE=  }}
-'''FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION'''
+==FUSARIUM OXYSPORUM TRYPSIN AT ATOMIC RESOLUTION==
+<StructureSection load='1gdu' size='340' side='right'caption='[[1gdu]], [[Resolution|resolution]] 1.07&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1gdu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDU 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]] 1.07&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1gdu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdu OCA], [https://pdbe.org/1gdu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gdu RCSB], [https://www.ebi.ac.uk/pdbsum/1gdu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gdu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRYP_FUSOX TRYP_FUSOX]
+== 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/gd/1gdu_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=1gdu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site.
-==Overview==
+Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.,Rypniewski WR, Ostergaard PR, Norregaard-Madsen M, Dauter M, Wilson KS Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):8-19. PMID:11134922<ref>PMID:11134922</ref>
-The X-ray structure of F. oxysporum trypsin has been determined at atomic resolution, revealing electron density in the binding site which was interpreted as a peptide bound in the sites S1, S2 and S3. The structure, which was initially determined at 1.07 A resolution and 283 K, has an Arg in the S1 specificity pocket. The study was extended to 0.81 A resolution at 100 K using crystals soaked in Arg, Lys and Gln to study in greater detail the binding at the S1 site. The electron density in the binding site was compared between the different structures and analysed in terms of partially occupied and overlapping components of peptide, solvent water and possibly other chemical moieties. Arg-soaked crystals reveal a density more detailed but similar to the original structure, with the Arg side chain visible in the S1 pocket and residual peptide density in the S2 and S3 sites. The density in the active site is complex and not fully interpreted. Lys at high concentrations displaces Arg in the S1 pocket, while some main-chain density remains in sites S2 and S3. Gln has been shown not to bind. The free peptide in the S1-S3 sites binds in a similar way to the binding loop of BPTI or the inhibitory domain of the Alzheimer's beta-protein precursor, with some differences in the S1 site.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-GDU is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDU OCA].
+</div>
+<div class="pdbe-citations 1gdu" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding., Rypniewski WR, Ostergaard PR, Norregaard-Madsen M, Dauter M, Wilson KS, Acta Crystallogr D Biol Crystallogr. 2001 Jan;57(Pt 1):8-19. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11134922 11134922]
+*[[Trypsin 3D structures|Trypsin 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Fusarium oxysporum]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Trypsin]]
+[[Category: Dauter M]]
-[[Category: Dauter, M.]]
+[[Category: Noerregaard-Madsen M]]
-[[Category: Noerregaard-Madsen, M.]]
+[[Category: Oestergaard P]]
-[[Category: Oestergaard, P.]]
+[[Category: Rypniewski WR]]
-[[Category: Rypniewski, W R.]]
+[[Category: Wilson KS]]
-[[Category: Wilson, K S.]]
-[[Category: Beta-barrel]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 17:27:03 2008''