3ni3: Difference between revisions

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{{Seed}}
[[Image:3ni3.png|left|200px]]


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==54-Membered ring macrocyclic beta-sheet peptide==
The line below this paragraph, containing "STRUCTURE_3ni3", creates the "Structure Box" on the page.
<StructureSection load='3ni3' size='340' side='right'caption='[[3ni3]], [[Resolution|resolution]] 1.34&Aring;' 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'>[[3ni3]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NI3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NI3 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">X-ray diffraction, [[Resolution|Resolution]] 1.34&#8491;</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=4BF:4-BROMO-L-PHENYLALANINE'>4BF</scene>, <scene name='pdbligand=HAO:{[3-(HYDRAZINOCARBONYL)-4-METHOXYPHENYL]AMINO}(OXO)ACETIC+ACID'>HAO</scene>, <scene name='pdbligand=IPA:ISOPROPYL+ALCOHOL'>IPA</scene>, <scene name='pdbligand=ORN:L-ORNITHINE'>ORN</scene></td></tr>
{{STRUCTURE_3ni3|  PDB=3ni3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ni3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ni3 OCA], [https://pdbe.org/3ni3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ni3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ni3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ni3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
This paper describes the X-ray crystallographic structure of a designed cyclic beta-sheet peptide that forms a well-defined hydrogen-bonded dimer that mimics beta-sheet dimers formed by proteins. The 54-membered ring macrocyclic peptide (1a) contains molecular template and turn units that induce beta-sheet structure in a heptapeptide strand that forms the dimerization interface. The X-ray crystallographic structure reveals the structures of the two "Hao" amino acids that help template the beta-sheet structure and the two delta-linked ornithine turn units that link the Hao-containing template to the heptapeptide beta-strand. The Hao amino acids adopt a conformation that resembles a tripeptide in a beta-strand conformation, with one edge of the Hao unit presenting an alternating array of hydrogen-bond donor and acceptor groups in the same pattern as that of a tripeptide beta-strand. The delta-linked ornithines adopt a conformation that resembles a hydrogen-bonded beta-turn, in which the ornithine takes the place of the i+1 and i+2 residues. The dimers formed by macrocyclic beta-sheet 1a resemble the dimers of many proteins, such as defensin HNP-3, the lambda-Cro repressor, interleukin 8, and the ribonuclease H domain of HIV-1 reverse transcriptase. The dimers of 1a self-assemble in the solid state into a barrel-shaped trimer of dimers in which the three dimers are arranged in a triangular fashion. Molecular modeling in which one of the three dimers is removed and the remaining two dimers are aligned face-to-face provides a model of the dimers of dimers of closely related macrocyclic beta-sheet peptides that were observed in solution.


===54-Membered ring macrocyclic beta-sheet peptide===
X-ray crystallographic structure of an artificial beta-sheet dimer.,Khakshoor O, Lin AJ, Korman TP, Sawaya MR, Tsai SC, Eisenberg D, Nowick JS J Am Chem Soc. 2010 Aug 25;132(33):11622-8. PMID:20669960<ref>PMID:20669960</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 3ni3" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20669960 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20669960}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
3NI3 is a 12 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NI3 OCA].
[[Category: Eisenberg D]]
 
[[Category: Khakshoor O]]
==Reference==
[[Category: Korman TP]]
<ref group="xtra">PMID:20669960</ref><references group="xtra"/>
[[Category: Nowick JS]]
[[Category: Eisenberg, D.]]
[[Category: Sawaya MR]]
[[Category: Khakshoor, O.]]
[[Category: Korman, T P.]]
[[Category: Nowick, J S.]]
[[Category: Sawaya, M R.]]
[[Category: Artificial beta sheet dimer]]
[[Category: Unknown function]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 14:17:29 2010''

Latest revision as of 09:03, 15 November 2023

54-Membered ring macrocyclic beta-sheet peptide

3ni3, resolution 1.34Å

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