1nld

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[[Image:1nld.jpg|left|200px]]
 
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{{Structure
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==FAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITOPE OF GP41 FROM HIV-1==
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|PDB= 1nld |SIZE=350|CAPTION= <scene name='initialview01'>1nld</scene>, resolution 2.9&Aring;
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<StructureSection load='1nld' size='340' side='right'caption='[[1nld]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1nld]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NLD 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]] 2.9&#8491;</td></tr>
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|GENE=
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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=1nld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nld OCA], [https://pdbe.org/1nld PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nld RCSB], [https://www.ebi.ac.uk/pdbsum/1nld PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nld ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=
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== Evolutionary Conservation ==
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nld FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nld OCA], [http://www.ebi.ac.uk/pdbsum/1nld PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1nld RCSB]</span>
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[[Image:Consurf_key_small.gif|200px|right]]
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}}
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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/nl/1nld_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=1nld 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 structure of a Fab fragment of a monoclonal antibody (1583) that neutralizes a broad range of HIV-1 isolates has been solved by X-ray crystallography. This antibody is directed against a poliovirus/HIV-I chimaera which presents a conserved epitope of the envelope protein gp41. Crystals of 1583 were obtained in the space group P2(1)2(1)2(1) and the structure solved by molecular replacement. The model has been refined against all data in the range 10-2.9 A to a final crystallographic R factor of 0.198. The antigen-binding site features a well defined groove, typical of antibodies that bind to small antigens, created in part by a relatively short CDR H3. The variable regions of 1583 were sequenced and, given the hydrophilic nature of the epitope, revealed a surprising lack of charged residues in the CDR's. However, the antigen-binding cleft is indeed very polar, due in part to the presence of two charged residues that emanate from outside the recognized CDR's.
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'''FAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITOPE OF GP41 FROM HIV-1'''
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Structure of the Fab fragment from a neutralizing monoclonal antibody directed against an epitope of gp41 from HIV-1.,Davies C, Beauchamp JC, Emery D, Rawas A, Muirhead H Acta Crystallogr D Biol Crystallogr. 1997 Mar 1;53(Pt 2):186-94. PMID:15299953<ref>PMID:15299953</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1nld" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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The structure of a Fab fragment of a monoclonal antibody (1583) that neutralizes a broad range of HIV-1 isolates has been solved by X-ray crystallography. This antibody is directed against a poliovirus/HIV-I chimaera which presents a conserved epitope of the envelope protein gp41. Crystals of 1583 were obtained in the space group P2(1)2(1)2(1) and the structure solved by molecular replacement. The model has been refined against all data in the range 10-2.9 A to a final crystallographic R factor of 0.198. The antigen-binding site features a well defined groove, typical of antibodies that bind to small antigens, created in part by a relatively short CDR H3. The variable regions of 1583 were sequenced and, given the hydrophilic nature of the epitope, revealed a surprising lack of charged residues in the CDR's. However, the antigen-binding cleft is indeed very polar, due in part to the presence of two charged residues that emanate from outside the recognized CDR's.
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*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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1NLD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NLD OCA].
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__TOC__
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</StructureSection>
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==Reference==
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[[Category: Large Structures]]
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Structure of the Fab fragment from a neutralizing monoclonal antibody directed against an epitope of gp41 from HIV-1., Davies C, Beauchamp JC, Emery D, Rawas A, Muirhead H, Acta Crystallogr D Biol Crystallogr. 1997 Mar 1;53(Pt 2):186-94. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299953 15299953]
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[[Category: Mus musculus]]
[[Category: Mus musculus]]
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[[Category: Single protein]]
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[[Category: Beauchamp JC]]
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[[Category: Beauchamp, J C.]]
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[[Category: Davies C]]
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[[Category: Davies, C.]]
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[[Category: Emery D]]
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[[Category: Emery, D.]]
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[[Category: Muirhead H]]
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[[Category: Muirhead, H.]]
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[[Category: Rawas A]]
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[[Category: Rawas, A.]]
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[[Category: fab fragment]]
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[[Category: immunoglobulin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:32:00 2008''
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Current revision

FAB FRAGMENT OF A NEUTRALIZING ANTIBODY DIRECTED AGAINST AN EPITOPE OF GP41 FROM HIV-1

PDB ID 1nld

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