2d3f: Difference between revisions

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-{{Seed}}
-[[Image:2d3f.png|left|200px]]
-<!--
+==Crystal structures of collagen model peptides (Pro-Pro-Gly)4-Pro-Hyp-Gly-(Pro-Pro-Gly)4==
-The line below this paragraph, containing "STRUCTURE_2d3f", creates the "Structure Box" on the page.
+<StructureSection load='2d3f' size='340' side='right'caption='[[2d3f]], [[Resolution|resolution]] 1.26&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'>[[2d3f]] is a 6 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=2D3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3F 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]] 1.26&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HYP:4-HYDROXYPROLINE'>HYP</scene></td></tr>
-{{STRUCTURE_2d3f|  PDB=2d3f  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3f OCA], [https://pdbe.org/2d3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3f RCSB], [https://www.ebi.ac.uk/pdbsum/2d3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3f ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q80BK4_SHV2 Q80BK4_SHV2]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Structures of (Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4) (ppg9-XYG) where (Xaa, Yaa) = (Pro, Hyp), (Hyp, Pro) or (Hyp, Hyp) were analyzed at high resolution using synchrotron radiation. Molecular and crystal structures of these peptides are very similar to those of the (Pro-Pro-Gly)(9) peptide. The results obtained in this study, together with those obtained from related compounds, indicated the puckering propensity of the Hyp in the X position: (1) Hyp(X) residues involved in the Hyp(X):Pro(Y) stacking pairs prefer the down-puckering conformation, as in ppg9-OPG, and ppg9-OOG; (2) Hyp(X) residues involved in the Hyp(X):Hyp(Y) stacking pairs prefer the up-puckering conformation if there is no specific reason to adopt the down-puckering conformation. Water molecules in these peptide crystals are classified into two groups, the 1st and 2nd hydration waters. Water molecules in the 1st hydration group have direct hydrogen bonds with peptide oxygen atoms, whereas those in the 2nd hydration group do not. Compared with globular proteins, the number of water molecules in the 2nd hydration shell of the ppg9-XYG peptides is very large, likely due to the unique rod-like molecular structure of collagen model peptides. In the collagen helix, the amino acid residues in the X and Y positions must protrude outside of the triple helix, which forces even the hydrophobic side chains, such as Pro, to be exposed to the surrounding water molecules. Therefore, most of the waters in the 2nd hydration shell are covering hydrophobic Pro side chains by forming clathrate structures. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 361-372, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.
-===Crystal structures of collagen model peptides (Pro-Pro-Gly)4-Pro-Hyp-Gly-(Pro-Pro-Gly)4===
+High-resolution structures of collagen-like peptides [(Pro-Pro-Gly)(4)-Xaa-Yaa-Gly-(Pro-Pro-Gly)(4)]: Implications for triple-helix hydration and Hyp(X) puckering.,Okuyama K, Hongo C, Wu G, Mizuno K, Noguchi K, Ebisuzaki S, Tanaka Y, Nishino N, Bachinger HP Biopolymers. 2009 May;91(5):361-72. PMID:19137577<ref>PMID:19137577</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2d3f" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19137577}}, adds the Publication Abstract to the page
+*[[Collagen 3D structures|Collagen 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19137577 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_19137577}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-D3F is a 6 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3F OCA].
+[[Category: Saimiriine gammaherpesvirus 2]]
+[[Category: Ebisuzaki S]]
-==Reference==
+[[Category: Nishino N]]
-<ref group="xtra">PMID:19137577</ref><references group="xtra"/>
+[[Category: Noguchi K]]
-[[Category: Ebisuzaki, S.]]
+[[Category: Okuyama K]]
-[[Category: Nishino, N.]]
+[[Category: Wu G]]
-[[Category: Noguchi, K.]]
-[[Category: Okuyama, K.]]
-[[Category: Wu, G.]]
-[[Category: Collagen]]
-[[Category: Crystal structure]]
-[[Category: Hydroxyproline]]
-[[Category: Structural protein]]
-[[Category: Triple-helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:39:58 2010''