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Yorodumi- PDB-1nzm: NMR structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nzm | ||||||||||||||||||
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Title | NMR structure of the parallel-stranded DNA quadruplex d(TTAGGGT)4 complexed with the telomerase inhibitor RHPS4 | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / Quadruplex DNA / telomeres / telomerase inhibition / NMR spectroscopy / molecular dynamics / drug-DNA interaction / TTAGGGT REPEAT | Function / homology | : / Chem-LG1 / DNA | Function and homology information Method | SOLUTION NMR / Restrained molecular dynamics | Authors | Gavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S. | Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Drug Recognition and Stabilisation of the Parallel-stranded DNA Quadruplex d(TTAGGGT)4 Containing the Human Telomeric Repeat Authors: Gavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S. #1: Journal: ANGEW.CHEM.INT.ED.ENGL. / Year: 2001 Title: Recognition and stabilisation of Quadruplex DNA by a potent new telomerase inhibitor: NMR studies of the 2:1 complex of a pentacyclic Methylacridinium cation with (TTAGGGT)4 Authors: Gavathiotis, E. / Heald, R.A. / Stevens, M.F.G. / Searle, M.S. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nzm.cif.gz | 219.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nzm.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 1nzm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nzm_validation.pdf.gz | 470.8 KB | Display | wwPDB validaton report |
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Full document | 1nzm_full_validation.pdf.gz | 687.1 KB | Display | |
Data in XML | 1nzm_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 1nzm_validation.cif.gz | 41.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/1nzm ftp://data.pdbj.org/pub/pdb/validation_reports/nz/1nzm | HTTPS FTP |
-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: 2168.445 Da / Num. of mol.: 4 / Source method: obtained synthetically #2: Chemical | #3: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: This structure was determined using standard 2D NMR techniques |
-Sample preparation
Details | Contents: 1.6mM 2:1 RHPS4-d(TTAGGGT)4, 100 mM KCl, 10 mM K2HPO4 buffer, 1 mM EDTA,90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | pH: 7.0 / Pressure: 1 atm / Temperature: 318 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Restrained molecular dynamics / Software ordinal: 1 Details: The structures are based on a set of 668 NOE restraints, 161 per strand of the quadruplex DNA (TTAGGGT)4 and 24 for both RHPS4 ligands.No hydrogen-bond restraints used. | ||||||||||||||||||
NMR representative | Selection criteria: fewest violation | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 10 |