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| | ==Deglucobalhimycin in complex with cell wall pentapeptide== | | ==Deglucobalhimycin in complex with cell wall pentapeptide== |
| - | <StructureSection load='1hhz' size='340' side='right' caption='[[1hhz]], [[Resolution|resolution]] 0.99Å' scene=''> | + | <StructureSection load='1hhz' size='340' side='right'caption='[[1hhz]], [[Resolution|resolution]] 0.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1hhz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1HHZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1HHZ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1hhz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Amycolatopsis_sp. Amycolatopsis sp.] 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=1HHZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HHZ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DVC:(2R,4S,6S)-4-AZANYL-4,6-DIMETHYL-OXANE-2,5,5-TRIOL'>DVC</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</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]] 0.99Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3FG:(2S)-AMINO(3,5-DIHYDROXYPHENYL)ETHANOIC+ACID'>3FG</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></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=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DVC:(2R,4S,6S)-4-AZANYL-4,6-DIMETHYL-OXANE-2,5,5-TRIOL'>DVC</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=PGR:R-1,2-PROPANEDIOL'>PGR</scene>, <scene name='pdbligand=PRD_000485:Deglucobalhimycin'>PRD_000485</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1go6|1go6]], [[1hhy|1hhy]], [[1hhu|1hhu]]</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=1hhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hhz OCA], [https://pdbe.org/1hhz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hhz RCSB], [https://www.ebi.ac.uk/pdbsum/1hhz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hhz ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1hhz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hhz OCA], [http://pdbe.org/1hhz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1hhz RCSB], [http://www.ebi.ac.uk/pdbsum/1hhz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1hhz ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bunkoczi, G]] | + | [[Category: Amycolatopsis sp]] |
| - | [[Category: Lehmann, C]] | + | [[Category: Large Structures]] |
| - | [[Category: Sheldrick, G M]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Vertesy, L]] | + | [[Category: Bunkoczi G]] |
| - | [[Category: Antibiotic]] | + | [[Category: Lehmann C]] |
| - | [[Category: Antibiotic-peptide complex]] | + | [[Category: Sheldrick GM]] |
| - | [[Category: Balhimycin]] | + | [[Category: Vertesy L]] |
| - | [[Category: Cell wall peptide]]
| + | |
| - | [[Category: Glycopeptide]]
| + | |
| Structural highlights
1hhz is a 6 chain structure with sequence from Amycolatopsis sp. and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 0.99Å |
| Ligands: | , , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
The vancomycin-related antibiotics balhimycin and degluco-balhimycin have been crystallized in complexes with di-, tri- and pentapeptides that emulate bacterial cell-wall precursors, and four structures determined at atomic resolution (<1 A). In addition to the features expected from previous structural and spectroscopic studies, two new motifs were observed that may prove important in the design of antibiotics modified to overcome bacterial resistance. A changed binding mode was found in two dipeptide complexes, and a new type of face-to-face oligomerization (in addition to the well-established back-to-back dimerization) was seen when the model peptide reaches a critical fraction of the size of the cell-wall precursor pentapeptide. The extensive interactions involving both antibiotic and peptide molecules in this interface should appreciably enhance the kinetic and thermodynamic stability of the complexes. In the pentapeptide complex, the relative positions of the peptides are close to those required for d-Ala elimination, so this structure may provide a realistic model for the prevention of the enzyme-catalyzed cell-wall crosslinking by antibiotic binding.
Structures of glycopeptide antibiotics with peptides that model bacterial cell-wall precursors.,Lehmann C, Bunkoczi G, Vertesy L, Sheldrick GM J Mol Biol. 2002 May 3;318(3):723-32. PMID:12054818[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lehmann C, Bunkoczi G, Vertesy L, Sheldrick GM. Structures of glycopeptide antibiotics with peptides that model bacterial cell-wall precursors. J Mol Biol. 2002 May 3;318(3):723-32. PMID:12054818 doi:10.1016/S0022-2836(02)00146-8
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