1b4z

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[[Image:1b4z.gif|left|200px]]
 
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{{Structure
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==OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK==
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|PDB= 1b4z |SIZE=350|CAPTION= <scene name='initialview01'>1b4z</scene>, resolution 1.75&Aring;
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<StructureSection load='1b4z' size='340' side='right'caption='[[1b4z]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IUM:URANYL+(VI)+ION'>IUM</scene>
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<table><tr><td colspan='2'>[[1b4z]] 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=1B4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4Z FirstGlance]. <br>
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|ACTIVITY=
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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|GENE= OPPA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=602 Salmonella typhimurium])
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<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=IUM:URANYL+(VI)+ION'>IUM</scene></td></tr>
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|DOMAIN=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4z OCA], [https://pdbe.org/1b4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4z RCSB], [https://www.ebi.ac.uk/pdbsum/1b4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4z ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4z OCA], [http://www.ebi.ac.uk/pdbsum/1b4z PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1b4z RCSB]</span>
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== Function ==
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}}
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[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.
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== Evolutionary Conservation ==
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'''OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b4z_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=1b4z ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.
Isothermal titration calorimetry has been used to study the binding of 20 different peptides to the peptide binding protein OppA, and the crystal structures of the ligand complexes have been refined. This periplasmic binding protein, part of the oligopeptide permease system of Gram negative bacteria, has evolved to bind and enclose small peptides of widely varying sequences. The peptides used in this study have the sequence Lys-X-Lys, where X is any of the 20 commonly occurring amino acids. The various side-chains found at position 2 on the ligand fit into a hydrated pocket. The majority of side-chains are restrained to particular conformations within the pocket. Water molecules act as flexible adapters, matching the hydrogen-bonding requirements of the protein and ligand and shielding charges on the buried ligand. This use of water by OppA to broaden the repertoire of its binding site is not unique, but contrasts sharply with other proteins which use water to help bind ligands highly selectively. Predicting the thermodynamics of binding from the structure of the complexes is highly complicated by the influence of water on the system.
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==About this Structure==
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Crystallographic and calorimetric analysis of peptide binding to OppA protein.,Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:10438628<ref>PMID:10438628</ref>
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1B4Z is a [[Single protein]] structure of sequence 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=1B4Z OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Crystallographic and calorimetric analysis of peptide binding to OppA protein., Sleigh SH, Seavers PR, Wilkinson AJ, Ladbury JE, Tame JR, J Mol Biol. 1999 Aug 13;291(2):393-415. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10438628 10438628]
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</div>
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[[Category: Salmonella typhimurium]]
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<div class="pdbe-citations 1b4z" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Sleigh, S H.]]
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[[Category: Tame, J R.H.]]
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[[Category: Wilkinson, A J.]]
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[[Category: complex (peptide transport/peptide)]]
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[[Category: peptide transport]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:53:45 2008''
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==See Also==
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*[[ABC transporter 3D structures|ABC transporter 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Salmonella enterica subsp. enterica serovar Typhimurium]]
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[[Category: Sleigh SH]]
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[[Category: Tame JRH]]
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[[Category: Wilkinson AJ]]

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OLIGO-PEPTIDE BINDING PROTEIN (OPPA) COMPLEXED WITH KDK

PDB ID 1b4z

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