This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1xj9

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

Structural highlights

1xj9 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A(3) forms a noncanonical base pair with A(8) in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network.,Petersson B, Nielsen BB, Rasmussen H, Larsen IK, Gajhede M, Nielsen PE, Kastrup JS J Am Chem Soc. 2005 Feb 9;127(5):1424-30. PMID:15686374^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Petersson B, Nielsen BB, Rasmussen H, Larsen IK, Gajhede M, Nielsen PE, Kastrup JS. Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network. J Am Chem Soc. 2005 Feb 9;127(5):1424-30. PMID:15686374 doi:10.1021/ja0458726

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1xj9"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:1xj9.png|left|200px]]
-<!--
+==Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network==
-The line below this paragraph, containing "STRUCTURE_1xj9", creates the "Structure Box" on the page.
+<StructureSection load='1xj9' size='340' side='right'caption='[[1xj9]], [[Resolution|resolution]] 2.60&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'>[[1xj9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XJ9 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]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=APN:2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-ADENINE'>APN</scene>, <scene name='pdbligand=CPN:2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-CYTOSINE'>CPN</scene>, <scene name='pdbligand=GPN:2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-GUANINE'>GPN</scene>, <scene name='pdbligand=TPN:2-AMINOETHYLGLYCINE-CARBONYLMETHYLENE-THYMINE'>TPN</scene></td></tr>
-{{STRUCTURE_1xj9|  PDB=1xj9  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xj9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xj9 OCA], [https://pdbe.org/1xj9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xj9 RCSB], [https://www.ebi.ac.uk/pdbsum/1xj9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xj9 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The X-ray structure of a partly self-complementary peptide nucleic acid (PNA) decamer (H-GTAGATCACT-l-Lys-NH(2)) to 2.60 A resolution is reported. The structure is mainly controlled by the canonical Watson-Crick base pairs formed by the self-complementary stretch of four bases in the middle of the decamer (G(4)A(5)T(6)C(7)). One right- and one left-handed Watson-Crick duplex are formed. The two PNA units C(9)T(10) change helical handedness, so that each PNA strand contains both a right- and a left-handed section. The changed handedness in C(9)T(10) allows formation of Hoogsteen hydrogen bonding between C(9)T(10) and G(4)A(5) of a PNA strand in an adjacent Watson-Crick double helix of the same handedness. Thereby, a PNA-PNA-PNA triplex is formed. The PNA unit A(3) forms a noncanonical base pair with A(8) in a symmetry-related strand of opposite handedness; the base pair is of the A-A reverse Hoogsteen type. The structural diversity of this PNA demonstrates how the PNA backbone is able to adapt to structures governed by the stacking and hydrogen-bonding interactions between the nucleobases. The crystal structure further shows how PNA oligomers containing limited sequence complementarity may form complex hydrogen-bonding networks.
-===Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network===
+Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network.,Petersson B, Nielsen BB, Rasmussen H, Larsen IK, Gajhede M, Nielsen PE, Kastrup JS J Am Chem Soc. 2005 Feb 9;127(5):1424-30. PMID:15686374<ref>PMID:15686374</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_15686374}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1xj9" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 15686374 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15686374}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJ9 OCA].
+[[Category: Gajhede M]]
+[[Category: Kastrup JS]]
-==Reference==
+[[Category: Larsen IK]]
-Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network., Petersson B, Nielsen BB, Rasmussen H, Larsen IK, Gajhede M, Nielsen PE, Kastrup JS, J Am Chem Soc. 2005 Feb 9;127(5):1424-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15686374 15686374]
+[[Category: Nielsen BB]]
+[[Category: Nielsen PE]]
-Crystal structure of a peptide nucleic acid (PNA) duplex at 1.7 A resolution., Rasmussen H, Kastrup JS, Nielsen JN, Nielsen JM, Nielsen PE, Nat Struct Biol. 1997 Feb;4(2):98-101. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9033585 9033585]
+[[Category: Petersson B]]
-[[Category: Gajhede, M.]]
+[[Category: Rasmussen H]]
-[[Category: Kastrup, J S.]]
-[[Category: Larsen, I K.]]
-[[Category: Nielsen, B B.]]
-[[Category: Nielsen, P E.]]
-[[Category: Petersson, B.]]
-[[Category: Rasmussen, H.]]
-[[Category: Duplex-triplex complex]]
-[[Category: Left-handed]]
-[[Category: Partly self-complementary]]
-[[Category: Peptide nucleic acid]]
-[[Category: Pna]]
-[[Category: Right-handed]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:03:13 2008''

1xj9

From Proteopedia

Current revision

Crystal structure of a partly self-complementary peptide nucleic acid (PNA) oligomer showing a duplex-triplex network

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox