5bmf: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5bmf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BMF FirstGlance]. <br>
<table><tr><td colspan='2'>[[5bmf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BMF FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4TJ:2-(5-{1-[1-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)-4,15-dioxo-8,11-dioxa-5,14-diazaicosan-20-yl]-3,3-dimethyl-6-sulfo-1,3-dihydro-2H-indol-2-ylidene}penta-1,3-dien-1-yl)-1-ethyl-3,3-dimethyl-3H-indolium-5-sulfonate'>4TJ</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4TJ:2-(5-{1-[1-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)-4,15-dioxo-8,11-dioxa-5,14-diazaicosan-20-yl]-3,3-dimethyl-6-sulfo-1,3-dihydro-2H-indol-2-ylidene}penta-1,3-dien-1-yl)-1-ethyl-3,3-dimethyl-3H-indolium-5-sulfonate'>4TJ</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5bmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bmf OCA], [https://pdbe.org/5bmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bmf RCSB], [https://www.ebi.ac.uk/pdbsum/5bmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bmf ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5bmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bmf OCA], [https://pdbe.org/5bmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bmf RCSB], [https://www.ebi.ac.uk/pdbsum/5bmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bmf ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Knowledge of the three-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 A on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures.
MoFvAb: modeling the Fv region of antibodies.,Bujotzek A, Fuchs A, Qu C, Benz J, Klostermann S, Antes I, Georges G MAbs. 2015 Jul 15:0. PMID:26176812<ref>PMID:26176812</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5bmf" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>

Revision as of 07:21, 1 May 2024

Crystal Structure of a Theophylline binding antibody Fab fragment

5bmf, resolution 2.80Å

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