1b2h: Difference between revisions

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-{{Seed}}
-[[Image:1b2h.png|left|200px]]
-<!--
+==Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine==
-The line below this paragraph, containing "STRUCTURE_1b2h", creates the "Structure Box" on the page.
+<StructureSection load='1b2h' size='340' side='right'caption='[[1b2h]], [[Resolution|resolution]] 1.90&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'>[[1b2h]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B2H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B2H 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene>, <scene name='pdbligand=U1:URANIUM+ATOM'>U1</scene></td></tr>
-{{STRUCTURE_1b2h|  PDB=1b2h  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b2h OCA], [https://pdbe.org/1b2h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b2h RCSB], [https://www.ebi.ac.uk/pdbsum/1b2h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b2h ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/OPPA_SALTY OPPA_SALTY] This protein is a component of the oligopeptide permease, a binding protein-dependent transport system, it binds peptides up to five amino acids long with high affinity.
+== 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/b2/1b2h_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=1b2h ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The oligopeptide-binding protein OppA provides a useful model system for studying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X-ray crystallography. The tripeptides fall into three series of ligands, which have been designed to examine the effects of small changes to the central side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly due to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is proposed to arise from unfavorable electrostatic interactions in the pocket, including the disruption of a key salt bridge. Marked entropy-enthalpy compensation is found across the series, and some of the difficulties in designing tightly binding ligands have been highlighted.
-===Oligo-Peptide Binding Protein Complexed with Lysyl-Ornithyl-Lysine===
+Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes.,Davies TG, Hubbard RE, Tame JR Protein Sci. 1999 Jul;8(7):1432-44. PMID:10422831<ref>PMID:10422831</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1b2h" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10422831}}, adds the Publication Abstract to the page
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10422831 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10422831}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-B2H is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B2H OCA].
+[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
+[[Category: Davies TG]]
-==Reference==
+[[Category: Tame JRH]]
-<ref group="xtra">PMID:10422831</ref><references group="xtra"/>
-[[Category: Salmonella typhimurium]]
-[[Category: Davies, T G.]]
-[[Category: Tame, J R.H.]]
-[[Category: Peptide binding protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:55:14 2009''