1rl4: Difference between revisions

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-{{Seed}}
-[[Image:1rl4.png|left|200px]]
-<!--
+==Plasmodium falciparum peptide deformylase complex with inhibitor==
-The line below this paragraph, containing "STRUCTURE_1rl4", creates the "Structure Box" on the page.
+<StructureSection load='1rl4' size='340' side='right'caption='[[1rl4]], [[Resolution|resolution]] 2.18&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'>[[1rl4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_falciparum_3D7 Plasmodium falciparum 3D7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RL4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RL4 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]] 2.18&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BL5:2-{N-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC+ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE'>BL5</scene>, <scene name='pdbligand=BRR:(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC+ACID'>BRR</scene>, <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene></td></tr>
-{{STRUCTURE_1rl4|  PDB=1rl4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rl4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rl4 OCA], [https://pdbe.org/1rl4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rl4 RCSB], [https://www.ebi.ac.uk/pdbsum/1rl4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rl4 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q8I372_PLAF7 Q8I372_PLAF7]
+== 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/rl/1rl4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1rl4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An altered version of peptide deformylase from Plasmodium falciparum (PfPDF), the organism that causes the most devastating form of malaria, has been cocrystallized with a synthesized inhibitor that has submicromolar affinity for its target protein. The structure is solved at 2.2 A resolution, an improvement over the 2.8 A resolution achieved during the structural determination of unliganded PfPDF. This represents the successful outcome of modifying the protein construct in order to overcome adverse crystal contacts and other problems encountered in the study of unliganded PfPDF. Two molecules of PfPDF are found in the asymmetric unit of the current structure. The active site of each monomer of PfPDF is occupied by a proteolyzed fragment of the tripeptide-like inhibitor. Unexpectedly, each PfPDF subunit is associated with two nearly complete molecules of the inhibitor, found at a protein-protein interface. This is the first structure of a eukaryotic PDF protein, a potential drug target, in complex with a ligand.
-===Plasmodium falciparum peptide deformylase complex with inhibitor===
+An improved crystal form of Plasmodium falciparum peptide deformylase.,Robien MA, Nguyen KT, Kumar A, Hirsh I, Turley S, Pei D, Hol WG Protein Sci. 2004 Apr;13(4):1155-63. Epub 2004 Mar 9. PMID:15010544<ref>PMID:15010544</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15010544}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1rl4" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15010544 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15010544}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-RL4 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Plasmodium_falciparum_3d7 Plasmodium falciparum 3d7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RL4 OCA].
+[[Category: Plasmodium falciparum 3D7]]
+[[Category: Hirsh I]]
-==Reference==
+[[Category: Hol WGJ]]
-An improved crystal form of Plasmodium falciparum peptide deformylase., Robien MA, Nguyen KT, Kumar A, Hirsh I, Turley S, Pei D, Hol WG, Protein Sci. 2004 Apr;13(4):1155-63. Epub 2004 Mar 9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15010544 15010544]
+[[Category: Kumar A]]
-[[Category: Formylmethionine deformylase]]
+[[Category: Nguyen KT]]
-[[Category: Plasmodium falciparum 3d7]]
+[[Category: Pei D]]
-[[Category: Single protein]]
+[[Category: Robien MA]]
-[[Category: Hirsh, I.]]
+[[Category: Turley S]]
-[[Category: Hol, W G.J.]]
-[[Category: Kumar, A.]]
-[[Category: Nguyen, K T.]]
-[[Category: Pei, D.]]
-[[Category: Robien, M A.]]
-[[Category: Turley, S.]]
-[[Category: Crystal engineering]]
-[[Category: Drug design]]
-[[Category: Malaria]]
-[[Category: Pdf]]
-[[Category: Peptide deformylase]]
-[[Category: Plasmodium]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:32:59 2008''