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1wz1

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Revision as of 16:40, 11 April 2018

Crystal structure of the Fv fragment complexed with dansyl-lysine

Structural highlights

1wz1 is a 2 chain structure with sequence from Lk3 transgenic mice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	1dlf, 2dlf
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Antigen-induced structural changes in the Fv fragment of an anti-dansyl immunoglobulin G were studied by X-ray crystallography and stopped-flow fluorescence measurement. The crystal structure of the Fv fragment complexed with dansyl-lysine was determined at a resolution of 1.85 A. The dansyl-lysine molecule bound to a narrow cavity formed by the complementarity-determining regions H3 and H1, the N-terminal region of the VH domain and L2 of the VL domain. The structure of the binding site in the crystal structure explained well the results of the previous nuclear magnetic resonance measurements. The hapten binding caused remarkable conformational changes in H3 and its environmental structures, including the hydration structure from those observed in the unliganded state. The tip of H3 moved about 12 A from its position in the unliganded state. In addition, because of the contacts of H3 with the VL domain at the domain interface, the conformational changes of H3 resulted in the relative rotation of the variable domains by 5 degrees from their association observed in the unliganded state. The hydrophobic interactions at the domain interface seemed to be particularly important for the mutual rotation of the domains. The stopped-flow fluorescence measurement monitoring the interaction of the dansyl group and the binding pocket revealed that H3 was in a conformational equilibrium of three consecutive conformational states in the presence of dansyl-lysine in solution; an unliganded state preventing the access of the hapten, another unliganded state able to bind the hapten and the complex. The conformational dynamics of H3 in recognizing and binding the hapten molecule are discussed on the basis of the structural information from the present and previous studies.

Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten.,Nakasako M, Oka T, Mashumo M, Takahashi H, Shimada I, Yamaguchi Y, Kato K, Arata Y J Mol Biol. 2005 Aug 19;351(3):627-40. PMID:16019026^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Nakasako M, Oka T, Mashumo M, Takahashi H, Shimada I, Yamaguchi Y, Kato K, Arata Y. Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten. J Mol Biol. 2005 Aug 19;351(3):627-40. PMID:16019026 doi:10.1016/j.jmb.2005.06.018

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wz1"

@@ Line 1: / Line 1: @@
 ==Crystal structure of the Fv fragment complexed with dansyl-lysine==
 <StructureSection load='1wz1' size='340' side='right' caption='[[1wz1]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
@@ Line 5: / Line 6: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DNS:N~6~-{[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}-L-LYSINE'>DNS</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dlf|1dlf]], [[2dlf|2dlf]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wz1 OCA], [http://pdbe.org/1wz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wz1 RCSB], [http://www.ebi.ac.uk/pdbsum/1wz1 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wz1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wz1 OCA], [http://pdbe.org/1wz1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wz1 RCSB], [http://www.ebi.ac.uk/pdbsum/1wz1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wz1 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wz/1wz1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wz/1wz1_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1wz1

From Proteopedia

Revision as of 16:40, 11 April 2018

Crystal structure of the Fv fragment complexed with dansyl-lysine

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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