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== | ==NMR structure of asymmetric homodimer of a82846b, a glycopeptide antibiotic, complexed with its cell wall pentapeptide fragment== | ||
<StructureSection load='1gac' size='340' side='right'caption='[[1gac]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1gac]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_orientalis Amycolatopsis orientalis]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GAC FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FGA:GAMMA-D-GLUTAMIC+ACID'>FGA</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=MLU:N-METHYL-D-LEUCINE'>MLU</scene>, <scene name='pdbligand=OMY:(BETAR)-3-CHLORO-BETA-HYDROXY-L-TYROSINE'>OMY</scene>, <scene name='pdbligand=OMZ:(BETAR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE'>OMZ</scene>, <scene name='pdbligand=PRD_000203:Chloroorienticin+A'>PRD_000203</scene>, <scene name='pdbligand=RER:(1R,3S,4S,5S)-3-AMINO-2,3,6-TRIDEOXY-3-METHYL-ALPHA-L-ARABINO-HEXOPYRANOSE'>RER</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=1gac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gac OCA], [https://pdbe.org/1gac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gac RCSB], [https://www.ebi.ac.uk/pdbsum/1gac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gac ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols. These structures were subsequently refined using the full CHARMm potential and the addition of water molecules in the calculation. The CHARMm structures occupied more conformational space than did the X-PLOR structures and were utilized for the structure analysis. From the structures, a unique set of interactions for the dALA-5 carboxylate pocket was observed, having backbone amides from residues 2 and 3 hydrogen bonding one carboxylate oxygen while amide 4 and the side chain amide from Asn-3 hydrogen bond the other oxygen. Also, near the N-terminal region of the ligand, the GGLU-2's carboxylate forms a hydrogen bond with the asymmetric disaccharide dyad, which helps to define the interactions seen for this part of the ligand. | Proton NMR assignments were determined for the asymmetric dimer complex of A82846B with the pentapeptide cell-wall fragment. A total of 683 experimental constraints, both distance and dihedral, were collected from NOESY and COSY data sets. From these constraints, a total of 80 structures were calculated using standard X-PLOR protocols. These structures were subsequently refined using the full CHARMm potential and the addition of water molecules in the calculation. The CHARMm structures occupied more conformational space than did the X-PLOR structures and were utilized for the structure analysis. From the structures, a unique set of interactions for the dALA-5 carboxylate pocket was observed, having backbone amides from residues 2 and 3 hydrogen bonding one carboxylate oxygen while amide 4 and the side chain amide from Asn-3 hydrogen bond the other oxygen. Also, near the N-terminal region of the ligand, the GGLU-2's carboxylate forms a hydrogen bond with the asymmetric disaccharide dyad, which helps to define the interactions seen for this part of the ligand. | ||
Conformation of A82846B, a glycopeptide antibiotic, complexed with its cell wall fragment: an asymmetric homodimer determined using NMR spectroscopy.,Prowse WG, Kline AD, Skelton MA, Loncharich RJ Biochemistry. 1995 Jul 25;34(29):9632-44. PMID:7626632<ref>PMID:7626632</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1gac" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Amycolatopsis orientalis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Kline AD]] | ||
[[Category: | [[Category: Loncharich RJ]] | ||
[[Category: Prowse WG]] | |||
[[Category: Skelton MA]] | |||