6idg
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==antibody 64M-5 Fab in complex with dT(6-4)T== | |
| + | <StructureSection load='6idg' size='340' side='right'caption='[[6idg]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[6idg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IDG FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5PY:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE'>5PY</scene>, <scene name='pdbligand=64T:5-HYDROXY-THYMIDINE-5-MONOPHOSPHATE'>64T</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=6idg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idg OCA], [https://pdbe.org/6idg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6idg RCSB], [https://www.ebi.ac.uk/pdbsum/6idg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6idg ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts produced by ultraviolet light are mutagenic and carcinogenic. The crystal structures of the anti-(6-4) photoproduct antibody 64M-5 Fab and of its complex with dT(6-4)T were determined at 2.5 and 2.0 A resolution, respectively. A comparison between the dT(6-4)T-liganded and unliganded structures indicates that the side chain of His93L is greatly rotated and shifted on binding to dT(6-4)T, leading to the formation of an electrostatic interaction with the phosphate moiety of dT(6-4)T, which shows a remarkable induced fit. Based on a comparison of the dT(6-4)T-liganded structures of the 64M-5 and 64M-2 Fabs, the electrostatic interaction between the side chain of His93L in 64M-5 and the phosphate moiety of dT(6-4)T is lost for Leu93L in 64M-2, while Arg90L in 64M-5 instead of Gln90L in 64M-2 stabilizes the conformation of complementarity-determining region (CDR) L3. These differences contribute to the higher affinity of 64M-5 for dT(6-4)T compared with that of 64M-2. | ||
| - | + | Structures of the antibody 64M-5 Fab and its complex with dT(6-4)T indicate induced-fit and high-affinity mechanisms.,Yokoyama H, Mizutani R, Noguchi S, Hayashida N Acta Crystallogr F Struct Biol Commun. 2019 Feb 1;75(Pt 2):80-88. doi:, 10.1107/S2053230X18017661. Epub 2019 Jan 23. PMID:30713158<ref>PMID:30713158</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 6idg" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: Hayashida | + | ==See Also== |
| - | [[Category: Noguchi | + | *[[Antibody 3D structures|Antibody 3D structures]] |
| + | *[[3D structures of non-human antibody|3D structures of non-human antibody]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Mus musculus]] | ||
| + | [[Category: Synthetic construct]] | ||
| + | [[Category: Hayashida N]] | ||
| + | [[Category: Mizutani R]] | ||
| + | [[Category: Noguchi S]] | ||
| + | [[Category: Yokoyama H]] | ||
Current revision
antibody 64M-5 Fab in complex with dT(6-4)T
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