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| | <StructureSection load='1w3m' size='340' side='right'caption='[[1w3m]], [[Resolution|resolution]] 1.00Å' scene=''> | | <StructureSection load='1w3m' size='340' side='right'caption='[[1w3m]], [[Resolution|resolution]] 1.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1w3m]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Actinoplanes_friuliensis Actinoplanes friuliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W3M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1W3M FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1w3m]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinoplanes_friuliensis Actinoplanes friuliensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W3M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W3M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=LNG:DELTA-3ISOTETRADECENOIC+ACID'>LNG</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]] 1Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2AS:(2S,3S)-3-METHYL-ASPARTIC+ACID'>2AS</scene>, <scene name='pdbligand=CPI:6-CARBOXYPIPERIDINE'>CPI</scene>, <scene name='pdbligand=VDL:(2R,3R)-2,3-DIAMINOBUTANOIC+ACID'>VDL</scene>, <scene name='pdbligand=VLL:(2S)-2,3-DIAMINOBUTANOIC+ACID'>VLL</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2AS:(2S,3S)-3-METHYL-ASPARTIC+ACID'>2AS</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CPI:6-CARBOXYPIPERIDINE'>CPI</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=LNG:DELTA-3ISOTETRADECENOIC+ACID'>LNG</scene>, <scene name='pdbligand=PRD_000487:Tsushimycin'>PRD_000487</scene>, <scene name='pdbligand=VDL:(2R,3R)-2,3-DIAMINOBUTANOIC+ACID'>VDL</scene>, <scene name='pdbligand=VLL:(2S)-2,3-DIAMINOBUTANOIC+ACID'>VLL</scene></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=1w3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w3m OCA], [http://pdbe.org/1w3m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1w3m RCSB], [http://www.ebi.ac.uk/pdbsum/1w3m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1w3m 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=1w3m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w3m OCA], [https://pdbe.org/1w3m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w3m RCSB], [https://www.ebi.ac.uk/pdbsum/1w3m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w3m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | [[Category: Actinoplanes friuliensis]] | | [[Category: Actinoplanes friuliensis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Bunkoczi, G]] | + | [[Category: Bunkoczi G]] |
| - | [[Category: Sheldrick, G M]] | + | [[Category: Sheldrick GM]] |
| - | [[Category: Vertesy, L]] | + | [[Category: Vertesy L]] |
| - | [[Category: Amphomycin]]
| + | |
| - | [[Category: Antibacterial]]
| + | |
| - | [[Category: Antibiotic]]
| + | |
| - | [[Category: Daptomycin]]
| + | |
| - | [[Category: Lipopetide]]
| + | |
| Structural highlights
1w3m is a 12 chain structure with sequence from Actinoplanes friuliensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1Å |
| Ligands: | , , , , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
The amphomycin derivative tsushimycin has been crystallized and its structure determined at 1.0 A resolution. The asymmetric unit contains 12 molecules and with 1300 independent atoms this structure is one of the largest solved using ab initio direct methods. The antibiotic is comprised of a cyclodecapeptide core, an exocyclic amino acid and a fatty-acid residue. Its backbone adopts a saddle-like conformation that is stabilized by a Ca2+ ion bound within the peptide ring and accounts for the Ca2+-dependence of this antibiotic class. Additional Ca2+ ions link the antibiotic molecules to dimers that enclose an empty space resembling a binding cleft. The dimers possess a large hydrophobic surface capable of interacting with the bacterial cell membrane. The antibiotic daptomycin may exhibit a similar conformation, as the amino-acid sequence is conserved at positions involved in Ca2+ binding.
Structure of the lipopeptide antibiotic tsushimycin.,Bunkoczi G, Vertesy L, Sheldrick GM Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1160-4. Epub 2005, Jul 20. PMID:16041082[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Bunkoczi G, Vertesy L, Sheldrick GM. Structure of the lipopeptide antibiotic tsushimycin. Acta Crystallogr D Biol Crystallogr. 2005 Aug;61(Pt 8):1160-4. Epub 2005, Jul 20. PMID:16041082 doi:S0907444905017270
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