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| - | [[Image:2b87.gif|left|200px]] | |
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| - | {{Structure
| + | ==Structural basis for molecular recognition in an affibody:affibody complex== |
| - | |PDB= 2b87 |SIZE=350|CAPTION= <scene name='initialview01'>2b87</scene>
| + | <StructureSection load='2b87' size='340' side='right'caption='[[2b87]]' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND=
| + | <table><tr><td colspan='2'>[[2b87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2B87 FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2b87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b87 OCA], [https://pdbe.org/2b87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2b87 RCSB], [https://www.ebi.ac.uk/pdbsum/2b87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2b87 ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=[[2b88|2B88]], [[2b89|2B89]]
| + | == Function == |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2b87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2b87 OCA], [http://www.ebi.ac.uk/pdbsum/2b87 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2b87 RCSB]</span> | + | [https://www.uniprot.org/uniprot/Q70AB8_STAAU Q70AB8_STAAU] |
| - | }}
| + | == Evolutionary Conservation == |
| - | | + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | '''Structural basis for molecular recognition in an affibody:affibody complex'''
| + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b8/2b87_consurf.spt"</scriptWhenChecked> |
| - | ==Overview== | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | Affibody molecules constitute a class of engineered binding proteins based on the 58-residue three-helix bundle Z domain derived from staphylococcal protein A (SPA). Affibody proteins are selected as binders to target proteins by phage display of combinatorial libraries in which typically 13 side-chains on the surface of helices 1 and 2 in the Z domain have been randomized. The Z(Taq):anti-Z(Taq) affibody-affibody complex, consisting of Z(Taq), originally selected as a binder to Taq DNA polymerase, and anti-Z(Taq), selected as binder to Z(Taq), is formed with a dissociation constant K(d) approximately 100 nM. We have determined high-precision solution structures of free Z(Taq) and anti-Z(Taq), and the Z(Taq):anti-Z(Taq) complex under identical experimental conditions (25 degrees C in 50 mM NaCl with 20 mM potassium phosphate buffer at pH 6.4). The complex is formed with helices 1 and 2 of anti-Z(Taq) in perpendicular contact with helices 1 and 2 of Z(Taq). The interaction surface is large ( approximately 1670 A(2)) and unusually non-polar (70 %) compared to other protein-protein complexes. It involves all varied residues on anti-Z(Taq), most corresponding (Taq DNA polymerase binding) side-chains on Z(Taq), and several additional side-chain and backbone contacts. Other notable features include a substantial rearrangement (induced fit) of aromatic side-chains in Z(Taq) upon binding, a close contact between glycine residues in the two subunits that might involve aliphatic glycine Halpha to backbone carbonyl hydrogen bonds, and four hydrogen bonds made by the two guanidinium N(eta)H(2) groups of an arginine side-chain. Comparisons of the present structure with other data for affibody proteins and the Z domain suggest that intrinsic binding properties of the originating SPA surface might be inherited by the affibody binders. A thermodynamic characterization of Z(Taq) and anti-Z(Taq) is presented in an accompanying paper.
| + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | | + | </jmolCheckbox> |
| - | ==About this Structure==
| + | </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=2b87 ConSurf]. |
| - | 2B87 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2B87 OCA].
| + | <div style="clear:both"></div> |
| - | | + | __TOC__ |
| - | ==Reference== | + | </StructureSection> |
| - | Structural basis for molecular recognition in an affibody:affibody complex., Lendel C, Dogan J, Hard T, J Mol Biol. 2006 Jun 23;359(5):1293-304. Epub 2006 May 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16750222 16750222]
| + | [[Category: Large Structures]] |
| - | [[Category: Protein complex]] | + | |
| | [[Category: Staphylococcus aureus]] | | [[Category: Staphylococcus aureus]] |
| - | [[Category: Dogan, J.]] | + | [[Category: Dogan J]] |
| - | [[Category: Hard, T.]] | + | [[Category: Hard T]] |
| - | [[Category: Lendel, C.]] | + | [[Category: Lendel C]] |
| - | [[Category: affibody]]
| + | |
| - | [[Category: induced fit]]
| + | |
| - | [[Category: molecular recognition]]
| + | |
| - | [[Category: nmr spectroscopy]]
| + | |
| - | [[Category: protein-protein interactions protein engineering]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:02:46 2008''
| + | |
