1dsr: Difference between revisions

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{{Seed}}
[[Image:1dsr.png|left|200px]]


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==Peptide antibiotic, NMR, 6 structures==
The line below this paragraph, containing "STRUCTURE_1dsr", creates the "Structure Box" on the page.
<StructureSection load='1dsr' size='340' side='right'caption='[[1dsr]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dsr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Actinoplanes_sp. Actinoplanes sp.]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DSR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DSR FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2TL:D-ALLOTHREONINE'>2TL</scene>, <scene name='pdbligand=AHB:BETA-HYDROXYASPARAGINE'>AHB</scene>, <scene name='pdbligand=ALO:ALLO-THREONINE'>ALO</scene>, <scene name='pdbligand=CHP:3-CHLORO-4-HYDROXYPHENYLGLYCINE'>CHP</scene>, <scene name='pdbligand=D4P:(2S)-AMINO(4-HYDROXYPHENYL)ACETIC+ACID'>D4P</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=FA7:(2Z,4E)-7-METHYLOCTA-2,4-DIENOIC+ACID'>FA7</scene>, <scene name='pdbligand=GHP:(2R)-AMINO(4-HYDROXYPHENYL)ETHANOIC+ACID'>GHP</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=ORD:D-ORNITHINE'>ORD</scene>, <scene name='pdbligand=PRD_000222:RAMOPLANIN+A2'>PRD_000222</scene></td></tr>
{{STRUCTURE_1dsr|  PDB=1dsr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dsr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dsr OCA], [https://pdbe.org/1dsr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dsr RCSB], [https://www.ebi.ac.uk/pdbsum/1dsr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dsr ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The 3D structure of ramoplanin was studied by NMR spectroscopy in aqueous solution. A total of 320 interproton distances were determined from a NOESY spectrum and were used as restraints in distance geometry calculations. A structural refinement was carried out by molecular dynamics calculations in a solvent box. The structure of ramoplanin is characterized by two antiparallel beta-strands which are formed by the residues 2-7 and 10-14, respectively. The beta-strands are connected by six intramolecular hydrogen bonds and a reverse beta-turn which is formed by Thr8 and Phe9 (in positions i+1 and i+2, respectively). Residues 2 and 14 are connected by a loop consisting of Leu15, Ala16, Chp17, and the side chain of Asn2. Although residues 14-17 show the formation of a beta-turn, only the N-terminal end of the turn is directly connected to one of the beta-strands (Gly14), whereas the C-terminal end (Chp17) is linked via the side chain of Asn2. The 3D conformation of ramoplanin is also stabilized by a hydrophobic cluster of the aromatic sidechains of the residues 3, 9, and 17. This hydrophobic collapse leads to a U-shaped topology of the beta-shee: with the beta-turn at one end and the loop at the other end. The structure found for ramoplanin differs corsiderably from the published structure of ramoplanose which might be due to a smaller number of NOE distance restraints used in the previous study.


===PEPTIDE ANTIBIOTIC, NMR, 6 STRUCTURES===
3D structure of ramoplanin: a potent inhibitor of bacterial cell wall synthesis.,Kurz M, Guba W Biochemistry. 1996 Sep 24;35(38):12570-5. PMID:8823194<ref>PMID:8823194</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1dsr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 8823194 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_8823194}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Actinoplanes sp]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DSR OCA].
[[Category: Large Structures]]
 
[[Category: Guba W]]
==Reference==
[[Category: Kurz M]]
3D structure of ramoplanin: a potent inhibitor of bacterial cell wall synthesis., Kurz M, Guba W, Biochemistry. 1996 Sep 24;35(38):12570-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8823194 8823194]
[[Category: Guba, W.]]
[[Category: Kurz, M.]]
[[Category: Antibiotic]]
[[Category: Inhibitor]]
[[Category: Ramoplanin]]
 
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