4p20
From Proteopedia
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structures of the bacterial ribosomal decoding site complexed with amikacin== | |
| + | <StructureSection load='4p20' size='340' side='right'caption='[[4p20]], [[Resolution|resolution]] 2.70Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[4p20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g5q 2g5q]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4P20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4P20 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]] 2.7Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKN:(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S+,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide'>AKN</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=4p20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4p20 OCA], [https://pdbe.org/4p20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4p20 RCSB], [https://www.ebi.ac.uk/pdbsum/4p20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4p20 ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Amikacin is the 4,6-linked aminoglycoside modified at position N1 of the 2-deoxystreptamine ring (ring II) by the L-haba group. In the present study, the crystal structure of a complex between oligonucleotide containing the bacterial ribosomal A site and amikacin has been solved at 2.7 A resolution. Amikacin specifically binds to the A site in practically the same way as its parent compound kanamycin. In addition, the L-haba group interacts with the upper side of the A site through two direct contacts, O2*...H-N4(C1496) and N4*-H...O6(G1497). The present crystal structure shows how the introduction of the L-haba group on ring II of aminoglycoside is an effective mutation for obtaining a higher affinity to the bacterial A site. | ||
| - | + | Crystal structure of the bacterial ribosomal decoding site complexed with amikacin containing the gamma-amino-alpha-hydroxybutyryl (haba) group.,Kondo J, Francois B, Russell RJ, Murray JB, Westhof E Biochimie. 2006 Aug;88(8):1027-31. Epub 2006 Jun 13. PMID:16806634<ref>PMID:16806634</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| + | </div> | ||
| + | <div class="pdbe-citations 4p20" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
| + | [[Category: Francois B]] | ||
| + | [[Category: Kondo J]] | ||
| + | [[Category: Murray JB]] | ||
| + | [[Category: Russell RJM]] | ||
| + | [[Category: Westhof E]] | ||
Current revision
Crystal structures of the bacterial ribosomal decoding site complexed with amikacin
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