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1wbf

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(New page: 200px<br /><applet load="1wbf" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wbf, resolution 2.30&Aring;" /> '''WINGED BEAN LECTIN, ...)
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[[Image:1wbf.jpg|left|200px]]<br /><applet load="1wbf" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wbf, resolution 2.30&Aring;" />
 
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'''WINGED BEAN LECTIN, SACCHARIDE FREE FORM'''<br />
 
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==Overview==
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==WINGED BEAN LECTIN, SACCHARIDE FREE FORM==
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The crystal structure of the saccharide-free form of the basic form of, winged-bean agglutinin (WBAI) has been solved by the molecular-replacement, method and refined at 2.3 A resolution. The final R factor is 19.7% for, all data in the resolution range 8.0-2.3 A. The asymmetric unit contains, two half-dimers, each located on a crystallographic twofold axis. The, structure of the saccharide-free form is compared with that of the complex, of WBAI with methyl-alpha-D-galactoside. The complex is composed of two, dimers in the asymmetric unit. The intersubunit interactions in the dimer, are nearly identical in the two structures. The binding site of the, saccharide-free structure contains three ordered water molecules at, positions similar to those of the hydroxyl groups of the carbohydrate, which are hydrogen bonded to the protein. Superposition of the, saccharide-binding sites of the two structures shows that the major, changes involve expulsion of these ordered water molecules and a shift of, about 0.6 A of the main-chain atoms of the variable loop.
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<StructureSection load='1wbf' size='340' side='right'caption='[[1wbf]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wbf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Psophocarpus_tetragonolobus Psophocarpus tetragonolobus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WBF FirstGlance]. <br>
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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]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
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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=1wbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wbf OCA], [https://pdbe.org/1wbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wbf RCSB], [https://www.ebi.ac.uk/pdbsum/1wbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wbf ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/LEC1_PSOTE LEC1_PSOTE] Lectin.
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wb/1wbf_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1wbf 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 ==
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The crystal structure of the saccharide-free form of the basic form of winged-bean agglutinin (WBAI) has been solved by the molecular-replacement method and refined at 2.3 A resolution. The final R factor is 19.7% for all data in the resolution range 8.0-2.3 A. The asymmetric unit contains two half-dimers, each located on a crystallographic twofold axis. The structure of the saccharide-free form is compared with that of the complex of WBAI with methyl-alpha-D-galactoside. The complex is composed of two dimers in the asymmetric unit. The intersubunit interactions in the dimer are nearly identical in the two structures. The binding site of the saccharide-free structure contains three ordered water molecules at positions similar to those of the hydroxyl groups of the carbohydrate which are hydrogen bonded to the protein. Superposition of the saccharide-binding sites of the two structures shows that the major changes involve expulsion of these ordered water molecules and a shift of about 0.6 A of the main-chain atoms of the variable loop.
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==About this Structure==
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Structure of basic winged-bean lectin and a comparison with its saccharide-bound form.,Manoj N, Srinivas VR, Suguna K Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):794-800. PMID:10089310<ref>PMID:10089310</ref>
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1WBF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Psophocarpus_tetragonolobus Psophocarpus tetragonolobus] with NAG, MN and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WBF 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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Structure of basic winged-bean lectin and a comparison with its saccharide-bound form., Manoj N, Srinivas VR, Suguna K, Acta Crystallogr D Biol Crystallogr. 1999 Apr;55(Pt 4):794-800. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10089310 10089310]
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</div>
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[[Category: Psophocarpus tetragonolobus]]
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<div class="pdbe-citations 1wbf" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Manoj, N.]]
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[[Category: Srinivas, V.R.]]
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[[Category: Suguna, K.]]
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[[Category: CA]]
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[[Category: MN]]
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[[Category: NAG]]
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[[Category: blood group specificity]]
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[[Category: lectin (agglutinin)]]
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[[Category: legume lectin]]
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[[Category: protein crystallography]]
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[[Category: saccharide free form]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:17:36 2007''
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==See Also==
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*[[Agglutinin 3D structures|Agglutinin 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: Psophocarpus tetragonolobus]]
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[[Category: Manoj N]]
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[[Category: Srinivas VR]]
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[[Category: Suguna K]]

Current revision

WINGED BEAN LECTIN, SACCHARIDE FREE FORM

PDB ID 1wbf

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