1ds2: Difference between revisions

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 <StructureSection load='1ds2' size='340' side='right'caption='[[1ds2]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ds2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Melga Melga] and [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DS2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ds2]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Meleagris_gallopavo Meleagris gallopavo] and [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DS2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DS2 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1LU:(2S)-2-HYDROXY-4-METHYL-PENTANOIC+ACID'>1LU</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3sgb|3sgb]], [[1sgr|1sgr]], [[1sgq|1sgq]], [[1sgp|1sgp]], [[2sgp|2sgp]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1LU:(2S)-2-HYDROXY-4-METHYL-PENTANOIC+ACID'>1LU</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Streptogrisin_B Streptogrisin B], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.81 3.4.21.81] </span></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=1ds2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ds2 OCA], [https://pdbe.org/1ds2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ds2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ds2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ds2 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PRTB_STRGR PRTB_STRGR]] Has a primary specificity for large aliphatic or aromatic amino acids.
+[https://www.uniprot.org/uniprot/PRTB_STRGR PRTB_STRGR] Has a primary specificity for large aliphatic or aromatic amino acids.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
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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=1ds2 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-X-ray crystallography has been used to determine the 3D structures of two complexes between Streptomyces griseus proteinase B (SGPB), a bacterial serine proteinase, and backbone variants of turkey ovomucoid third domain (OMTKY3). The natural P1 residue (Leu18I) has been substituted by a proline residue (OMTKY3-Pro18I) and in the second variant, the peptide bond between Thr17I and Leu18I was replaced by an ester bond (OMTKY3-psi[COO]-Leu18I). Both variants lack the P1 NH group that donates a bifurcated hydrogen bond to the carbonyl O of Ser214 and O(gamma) of the catalytic Ser195, one of the common interactions between serine proteinases and their canonical inhibitors. The SGPB:OMTKY3-Pro18I complex has many structural differences in the vicinity of the S1 pocket when compared with the previously determined structure of SGPB:OMTKY3-Leu18I. The result is a huge difference in the DeltaG degrees of binding (8.3 kcal/mol), only part of which can be attributed to the missing hydrogen bond. In contrast, very little structural difference exists between the complexes of SGPB:OMTKY3-psi[COO]-Leu18I and SGPB:OMTKY3-Leu18I, aside from an ester O replacing the P1 NH group. Therefore, the difference in DeltaG degrees, 1.5 kcal/mol as calculated from the measured equilibrium association constants, can be attributed to the contribution of the P1 NH hydrogen bond toward binding. A crystal structure of OMTKY3 having a reduced peptide bond between P1 Leu18I and P'1 Asp19I, (OMTKY3-psi[CH2NH2+]-Asp19I) has also been determined by X-ray crystallography. This variant has very weak association equilibrium constants with SGPB and with chymotrypsin. The structure of the free inhibitor suggests that the reduced peptide bond has not introduced any major structural changes in the inhibitor. Therefore, its poor ability to inhibit serine proteinases is likely due to the disruptions of the canonical interactions at the oxyanion hole.
-Contribution of peptide bonds to inhibitor-protease binding: crystal structures of the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3-psi[COO]-Leu18I in complex with Streptomyces griseus proteinase B (SGPB) and the structure of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I.,Bateman KS, Huang K, Anderson S, Lu W, Qasim MA, Laskowski M Jr, James MN J Mol Biol. 2001 Jan 26;305(4):839-49. PMID:11162096<ref>PMID:11162096</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ds2" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Proteinase|Proteinase]]
 *[[Proteinase 3D structures|Proteinase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Melga]]
+[[Category: Meleagris gallopavo]]
-[[Category: Streptogrisin B]]
 [[Category: Streptomyces griseus]]
-[[Category: Anderson, S]]
+[[Category: Anderson S]]
-[[Category: Bateman, K S]]
+[[Category: Bateman KS]]
-[[Category: Huang, K]]
+[[Category: Huang K]]
-[[Category: James, M N.G]]
+[[Category: James MNG]]
-[[Category: Laskowski, M]]
+[[Category: Laskowski Jr M]]
-[[Category: Lu, W]]
+[[Category: Lu W]]
-[[Category: Qasim, M A]]
+[[Category: Qasim MA]]
-[[Category: Canonical inhibitor]]
-[[Category: Ester bond]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
-[[Category: Omtky3]]
-[[Category: Ovomucoid]]
-[[Category: Protein inhibitor]]
-[[Category: Serine proteinase]]
-[[Category: Sgpb]]