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- PDB-1y8d: Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interfac... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1y8d | ||||||||||||||||||
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Title | Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interface, single-residue chain reversal loops and GAG triad in the context of A(GGGG) pentad | ||||||||||||||||||
![]() | 5'-D(*![]() DNA / DIMERIC PARALLEL-STRANDED QUADRUPLEX / DNA APTAMER / HIV-1 INTEGRASE INHIBITOR DESIGN / 3+1 G-TETRAD / SINGLE NUCLEOTIDE CHAIN REVERSAL LOOP / GAG TRIAD / (A)GGGG PENTAD | Function / homology | DNA / DNA (> 10) | ![]() Method | SOLUTION NMR / distance geometry; simulated annealing; molecular dynamics; matrix relaxation | ![]() Phan, A.T. / Kuryavyi, V.V. / Ma, J.-B. / Faure, A. / Andreola, M.-L. / Patel, D.J. | ![]() ![]() Title: An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase Authors: Phan, A.T. / Kuryavyi, V.V. / Ma, J.-B. / Faure, A. / Andreola, M.-L. / Patel, D.J. History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 202.9 KB | Display | ![]() |
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PDB format | ![]() | 169.1 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 301.2 KB | Display | ![]() |
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Full document | ![]() | 357.7 KB | Display | |
Data in XML | ![]() | 3.2 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 5140.312 Da / Num. of mol.: 2 / Fragment: HIV INTEGRASE INHIBITOR SEQUENCE / Source method: obtained synthetically Details: DNA aptamer obtained by SELEX of ODN inhibiting RNase H activity of HIV Reverse Transcriptase |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: The experiments 1H-15N HMBC, 1H-13C HMBC, 1H-13C HSQC, 1H-13C sHMBC were performed for assignments |
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Sample preparation
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Sample conditions | Ionic strength: 90 mM KCl / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: distance geometry; simulated annealing; molecular dynamics; matrix relaxation Software ordinal: 1 Details: the structures are based on a total of 1689 restraints, 283 are NOE-derived distance constraints, 3 negative restraints, 84 dihedral angle restraints,104 distance restraints from hydrogen ...Details: the structures are based on a total of 1689 restraints, 283 are NOE-derived distance constraints, 3 negative restraints, 84 dihedral angle restraints,104 distance restraints from hydrogen bonds, 243 intensity restraints (each of five mixing times) | ||||||||||||||||
NMR representative | Selection criteria: fewest violations,lowest energy | ||||||||||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted,back calculated data agree with experimental NOESY spectrum,structures with acceptable covalent geometry,structures with favorable non-bond energy Conformers calculated total number: 100 / Conformers submitted total number: 10 |