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Open data
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Basic information
Entry | Database: PDB / ID: 1hhx | ||||||
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Title | Solution structure of LNA3:RNA hybrid | ||||||
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![]() | ANTISENSE / LOCKED NUCLEIC ACID / LNA / RNA / HYBRID / RNASE H | ||||||
Function / homology | DNA/RNA hybrid / RNA![]() | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
![]() | Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P. | ||||||
![]() | ![]() Title: Locked Nucleic Acid (Lna) Recognition of RNA: NMR Solution Structures of Lna:RNA Hybrids Authors: Petersen, M. / Bondensgaard, K. / Wengel, J. / Jacobsen, J.P. #1: ![]() Title: Structural Studies of Lna:RNA Duplexes by NMR: Conformations and Implications for Rnase H Activity. Authors: Bondensgaard, K. / Petersen, M. / Singh, S.K. / Rajwanshi, V.K. / Kumar, R. / Wengel, J. / Jacobsen, J.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 389.5 KB | Display | ![]() |
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PDB format | ![]() | 320.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 339.2 KB | Display | ![]() |
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Full document | ![]() | 622.1 KB | Display | |
Data in XML | ![]() | 15.7 KB | Display | |
Data in CIF | ![]() | 26.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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NMR ensembles |
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Components
#1: DNA/RNA hybrid | Mass: 2814.843 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: RNA chain | Mass: 2855.767 Da / Num. of mol.: 1 / Source method: obtained synthetically |
Sequence details | CHAIN A RESIDUES 2,5,7 ARE LOCKED NUCLEIC ACIDS OR (1R,3R,4R,7S)-7-HYDROXY-1-HYDROXYMETHYL-3- ...CHAIN A RESIDUES 2,5,7 ARE LOCKED NUCLEIC ACIDS OR (1R,3R,4R,7S)-7-HYDROXY-1-HYDROXYMET |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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NMR experiment | Type: NOESY |
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Sample preparation
Details | Contents: 0.7E-3M LNA1:RNA, 0.1M NACL, 5E-5M EDTA AND 1E-2M PHOSPHATE BUFFER IN 100% D2O |
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Sample conditions | Ionic strength: 0.1 / pH: 7.0 / Pressure: 1 atm / Temperature: 298 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz |
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Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: A TOTAL OF 423 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. A FURTHER 58 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM NOESY IN H2O ...Details: A TOTAL OF 423 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM A FULL RELAXATION MATRIX ANALYSIS WITH THE PROGRAM RANDMARDI. A FURTHER 58 NOE DISTANCE RESTRAINTS WERE OBTAINED FROM NOESY IN H2O USING ISPA. 22 WATSON-CRICK BASE PAIRING RESTRAINTS. | |||||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 40 / Conformers submitted total number: 34 |