1ls5: Difference between revisions

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 <StructureSection load='1ls5' size='340' side='right'caption='[[1ls5]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ls5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Plafa Plafa]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jgf 1jgf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ls5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum Plasmodium falciparum] and [https://en.wikipedia.org/wiki/Streptomyces_argenteolus_subsp._toyonakensis Streptomyces argenteolus subsp. toyonakensis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jgf 1jgf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LS5 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</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]] 2.8&#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;'>[[1sme|1sme]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IVA:ISOVALERIC+ACID'>IVA</scene>, <scene name='pdbligand=STA:STATINE'>STA</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=1ls5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ls5 OCA], [https://pdbe.org/1ls5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ls5 RCSB], [https://www.ebi.ac.uk/pdbsum/1ls5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ls5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PLM4_PLAF7 PLM4_PLAF7] During the asexual blood stage, catalyzes the cleavage of denatured host hemoglobin (Hb) (By similarity). Digestion of host Hb is an essential step which provides the parasite with amino acids for protein synthesis, and regulates osmolarity (Probable).[UniProtKB:Q17SB3]
 == 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=1ls5 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Malaria remains a human disease of global significance and a major cause of high infant mortality in endemic nations. Parasites of the genus Plasmodium cause the disease by degrading human hemoglobin as a source of amino acids for their growth and maturation. Hemoglobin degradation is initiated by aspartic proteases, termed plasmepsins, with a cleavage at the alpha-chain between residues Phe33 and Leu34. Plasmepsin II is one of the four catalytically active plasmepsins that has been identified in the food vacuole of Plasmodium falciparum. Novel crystal structures of uncomplexed plasmepsin II as well as the complex with a potent inhibitor have been refined with data extending to resolution limits of 1.9A and 2.7A, and to R factors of 17% and 18%, respectively. The inhibitor, N-(3-[(2-benzo[1,3]dioxol-5-yl-ethyl)[3-(1-methyl-3-oxo-1,3-dihydro-isoind ol-2-yl)-propionyl]-amino]-1-benzyl-2-(hydroxypropyl)-4-benzyloxy-3,5-dime thoxy-benzamide, belongs to a family of potent non-peptidic inhibitors that have large P1' groups. Such inhibitors could not be modeled into the binding cavity of the structure of plasmepsin II in complex with pepstatin A. Our structures reveal that the binding cavities of the new complex and uncomplexed plasmepsin II are considerably more open than that of the pepstatin A complex, allowing for larger heterocyclic groups in the P1', P2' and P2 positions. Both complexed and uncomplexed plasmepsin II crystallized in space group P2, with one monomer in the asymmetric unit. The structures show extensive interlocking of monomers around the crystallographic axis of symmetry, with areas in excess of 2300A(2) buried at the interface, and a loop of one monomer interacting with the binding cavity of the 2-fold related monomer. Electron density for this loop is only fully ordered in the complexed structure.
-Novel uncomplexed and complexed structures of plasmepsin II, an aspartic protease from Plasmodium falciparum.,Asojo OA, Gulnik SV, Afonina E, Yu B, Ellman JA, Haque TS, Silva AM J Mol Biol. 2003 Mar 14;327(1):173-81. PMID:12614616<ref>PMID:12614616</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1ls5" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Plasmepsin|Plasmepsin]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Plafa]]
+[[Category: Plasmodium falciparum]]
-[[Category: Afonina, E]]
+[[Category: Streptomyces argenteolus subsp. toyonakensis]]
-[[Category: Asojo, O A]]
+[[Category: Afonina E]]
-[[Category: Ellman, J A]]
+[[Category: Asojo OA]]
-[[Category: Gulnik, S V]]
+[[Category: Ellman JA]]
-[[Category: Haque, T S]]
+[[Category: Gulnik SV]]
-[[Category: Silva, A M]]
+[[Category: Haque TS]]
-[[Category: Yu, B]]
+[[Category: Silva AM]]
-[[Category: Eukaryotic aspartic proteinase]]
+[[Category: Yu B]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]