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3b2c

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Current revision (09:57, 14 February 2024) (edit) (undo)
 
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<StructureSection load='3b2c' size='340' side='right'caption='[[3b2c]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
<StructureSection load='3b2c' size='340' side='right'caption='[[3b2c]], [[Resolution|resolution]] 1.36&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3b2c]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B2C FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3b2c]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Saimiriine_gammaherpesvirus_2 Saimiriine gammaherpesvirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B2C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B2C FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=HZP:(4S)-4-HYDROXY-L-PROLINE'>HZP</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.36&#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=HYP:4-HYDROXYPROLINE'>HYP</scene>, <scene name='pdbligand=HZP:(4S)-4-HYDROXY-L-PROLINE'>HZP</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=3b2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b2c OCA], [https://pdbe.org/3b2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b2c RCSB], [https://www.ebi.ac.uk/pdbsum/3b2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b2c 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=3b2c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b2c OCA], [https://pdbe.org/3b2c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b2c RCSB], [https://www.ebi.ac.uk/pdbsum/3b2c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b2c ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q80BK4_SHV2 Q80BK4_SHV2]
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Extensive studies on the structure of collagen have revealed that the hydroxylation of Pro residues in a variety of model peptides with the typical (X-Y-Gly)(n) repeats (X and Y: Pro and its analogues) represents one of the major factors influencing the stability of triple helices. While (2S,4R)-hydroxyproline (Hyp) at the position Y stabilizes the triple helix, (2S,4S)-hydroxyproline (hyp) at the X-position destabilizes the helix as demonstrated that the triple helix of (hyp-Pro-Gly)(15) is less stable than that of (Pro-Pro-Gly)(15) and that a shorter peptide (hyp-Pro-Gly)(10) does not form the helix. In order to clarify the role of the hydroxyl group of Pro residues to play in the stabilization mechanism of the collagen triple helix, we synthesized and crystallized a model peptide (Pro-Hyp-Gly)(4) -(hyp-Pro-Gly)(2) -(Pro-Hyp-Gly)(4) and analyzed its structure by X-ray crystallography and CD spectroscopy. In the crystal, the main-chain of this peptide forms a typical collagen like triple helix. The majority of hyp residues take down pucker with exceptionally shallow angles probably to relieve steric hindrance, but the remainders protrude the hydroxyl group towards solvent with the less favorable up pucker to fit in a triple helix. There is no indication of the existence of an intra-molecular hydrogen bond between the hydroxyl moiety and the carbonyl oxygen of hyp supposed to destabilize the triple helix. We also compared the conformational energies of up and down packers of the pyrrolidine ring in Ac-hyp-NMe(2) by quantum mechanical calculations. (c) 2011 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2011.
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The triple helical structure and stability of collagen model peptide with 4(S)-hydroxyprolyl-pro-gly units.,Motooka D, Kawahara K, Nakamura S, Doi M, Nishi Y, Nishiuchi Y, Kee Kang Y, Nakazawa T, Uchiyama S, Yoshida T, Ohkubo T, Kobayashi Y Biopolymers. 2011 Oct 24. doi: 10.1002/bip.21730. PMID:22020801<ref>PMID:22020801</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3b2c" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Doi, M]]
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[[Category: Saimiriine gammaherpesvirus 2]]
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[[Category: Kang, Y K]]
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[[Category: Doi M]]
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[[Category: Kawahara, K]]
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[[Category: Kang YK]]
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[[Category: Kobayashi, Y]]
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[[Category: Kawahara K]]
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[[Category: Motooka, D]]
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[[Category: Kobayashi Y]]
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[[Category: Nakamura, S]]
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[[Category: Motooka D]]
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[[Category: Nakazawa, T]]
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[[Category: Nakamura S]]
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[[Category: Nishi, Y]]
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[[Category: Nakazawa T]]
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[[Category: Nishiuchi, Y]]
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[[Category: Nishi Y]]
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[[Category: Ohkubo, T]]
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[[Category: Nishiuchi Y]]
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[[Category: Uchiyama, S]]
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[[Category: Ohkubo T]]
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[[Category: Yoshida, T]]
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[[Category: Uchiyama S]]
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[[Category: Amino acid-preference]]
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[[Category: Yoshida T]]
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[[Category: Collagen stability]]
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[[Category: Puckering]]
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[[Category: Structural protein]]
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[[Category: Triple helix]]
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Current revision

Crystal structure of the collagen triple helix model [{PRO-HYP(R)-GLY}4-{HYP(S)-Pro-GLY}2-{PRO-HYP(R)-GLY}4]3

PDB ID 3b2c

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