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Yorodumi- PDB-1y8d: Dimeric parallel-stranded tetraplex with 3+1 5' G-tetrad interfac... -
+Open data
-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 | ||||||||||||||||||
Components | 5'-D(*Keywords | 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) | Function and homology information Method | SOLUTION NMR / distance geometry; simulated annealing; molecular dynamics; matrix relaxation | Authors | Phan, A.T. / Kuryavyi, V.V. / Ma, J.-B. / Faure, A. / Andreola, M.-L. / Patel, D.J. | Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 | 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y8d.cif.gz | 201.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y8d.ent.gz | 175.6 KB | Display | PDB format |
PDBx/mmJSON format | 1y8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8d ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8d | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 |
-Sample preparation
Details |
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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 |