1d3x
From Proteopedia
| Line 1: | Line 1: | ||
| - | [[Image:1d3x.gif|left|200px]] | + | [[Image:1d3x.gif|left|200px]] |
| - | + | ||
| - | '''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES''' | + | {{Structure |
| + | |PDB= 1d3x |SIZE=350|CAPTION= <scene name='initialview01'>1d3x</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES''' | ||
| + | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | 1D3X is a [ | + | 1D3X 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=1D3X OCA]. |
==Reference== | ==Reference== | ||
| - | Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT)., Tarkoy M, Phipps AK, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5810-9. PMID:[http:// | + | Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT)., Tarkoy M, Phipps AK, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5810-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9558314 9558314] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Feigon, J.]] | [[Category: Feigon, J.]] | ||
| Line 20: | Line 29: | ||
[[Category: triplex]] | [[Category: triplex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:32:34 2008'' |
Revision as of 08:32, 20 March 2008
| |||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
INTRAMOLECULAR DNA TRIPLEX, NMR, 10 STRUCTURES
Overview
A DNA molecule was designed and synthesized with three octanucleotide stretches linked by two hexakis(ethylene glycol) chains to form an intramolecular triplex in solution. The structural data obtained from a series of NMR NOESY spectra yielded interproton distances, and COSY experiments provided dihedral angle information for analysis of deoxyribose ring pucker. Using distance geometry followed by simulated annealing with restrained molecular dynamics and relaxation matrix refinement, a well-refined ensemble of conformations was calculated. Although some NOE cross-peaks involving protons of the hexakis(ethylene glycol) linker could be identified, most could not be assigned and the conformations of the linkers were not determined. The deoxyribose conformations are predominantly of the S type, except for the protonated cytosine residues in the third strand which show hybrid N and S character. Overall, the duplex part of the molecule resembles a B-DNA double helix with the third strand bound in its major groove by Hoogsteen hydrogen bonds. This structure provides a basis for comparison with triplexes containing noncanonical or nonnatural nucleotides.
About this Structure
1D3X is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Solution structure of an intramolecular DNA triplex linked by hexakis(ethylene glycol) units: d(AGAGAGAA-(EG)6-TTCTCTCT-(EG)6-TCTCTCTT)., Tarkoy M, Phipps AK, Schultze P, Feigon J, Biochemistry. 1998 Apr 28;37(17):5810-9. PMID:9558314
Page seeded by OCA on Thu Mar 20 10:32:34 2008
