1pqt

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[[Image:1pqt.gif|left|200px]]
 
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{{Structure
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==REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS==
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|PDB= 1pqt |SIZE=350|CAPTION= <scene name='initialview01'>1pqt</scene>
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<StructureSection load='1pqt' size='340' side='right'caption='[[1pqt]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>
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<table><tr><td colspan='2'>[[1pqt]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PQT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PQT FirstGlance]. <br>
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|ACTIVITY=
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</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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|GENE=
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pqt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqt OCA], [https://pdbe.org/1pqt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pqt RCSB], [https://www.ebi.ac.uk/pdbsum/1pqt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pqt ProSAT]</span></td></tr>
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|DOMAIN=
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</table>
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|RELATEDENTRY=[[1kr8|1KR8]]
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<div style="background-color:#fffaf0;">
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1pqt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pqt OCA], [http://www.ebi.ac.uk/pdbsum/1pqt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1pqt RCSB]</span>
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== Publication Abstract from PubMed ==
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}}
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'''REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS'''
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==Overview==
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The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.
The structure of the 13C,15N-labeled d(GCGAAGC) hairpin, as determined by NMR spectroscopy and refined using molecular dynamics with NOE-derived distances, torsion angles, and residual dipolar couplings (RDCs), is presented. Although the studied molecule is of small size, it is demonstrated that the incorporation of diminutive RDCs can significantly improve local structure determination of regions undefined by the conventional restraints. Very good correlation between the experimental and back-calculated small one- and two-bond 1H-13C, 1H-15N, 13C-13C and 13C-15N coupling constants has been attained. The final structures clearly show typical features of the miniloop architecture. The structure is discussed in context of the extraordinary stability of the d(GCGAAGC) hairpin, which originates from a complex interplay between the aromatic base stacking and hydrogen bonding interactions.
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==About this Structure==
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Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings.,Padrta P, Stefl R, Kralik L, Zidek L, Sklenar V J Biomol NMR. 2002 Sep;24(1):1-14. PMID:12449414<ref>PMID:12449414</ref>
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1PQT is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PQT OCA].
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==Reference==
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Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings., Padrta P, Stefl R, Kralik L, Zidek L, Sklenar V, J Biomol NMR. 2002 Sep;24(1):1-14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12449414 12449414]
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[[Category: Protein complex]]
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[[Category: Padrta, P.]]
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[[Category: Sklenar, V.]]
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[[Category: Stefl, R.]]
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[[Category: Zidek, L.]]
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[[Category: dna]]
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[[Category: ga mismatch]]
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[[Category: hairpin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:03:18 2008''
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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 1pqt" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Padrta P]]
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[[Category: Sklenar V]]
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[[Category: Stefl R]]
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[[Category: Zidek L]]

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REFINEMENT OF d(GCGAAGC) HAIRPIN STRUCTURE USING ONE- AND TWO-BOND RESIDUAL DIPOLAR COUPLINGS

PDB ID 1pqt

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