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Yorodumi- PDB-1agu: THE SOLUTION NMR STRUCTURE OF THE C10R ADDUCT OF BENZO[A]PYRENE-D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1agu | |||||||||
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Title | THE SOLUTION NMR STRUCTURE OF THE C10R ADDUCT OF BENZO[A]PYRENE-DIOL-EPOXIDE AT THE N6 POSITION OF ADENINE OF AN 11 BASE-PAIR OLIGONUCLEOTIDE SEQUENCE CODING FOR AMINO ACIDS 60-62 OF THE PRODUCT OF THE N-RAS PROTOONCOGENE, MINIMIZED AVERAGE STRUCTURE | |||||||||
Components |
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Keywords | DNA / DNA DUPLEX / HUMAN N-RAS GENE / CODON 61 SEQUENCE / C10R-BPDE ADDUCT / INTERCALATION / N6-ADENINE ADDUCT / DEOXYRIBONUCLEIC ACID | |||||||||
Function / homology | DNA / DNA (> 10) Function and homology information | |||||||||
Method | SOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING | |||||||||
Authors | Zegar, I.S. / Stone, M.P. | |||||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Adduction of the human N-ras codon 61 sequence with (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene: structural refinement of the intercalated SRSR(61,2) (-)- ...Title: Adduction of the human N-ras codon 61 sequence with (-)-(7S,8R,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene: structural refinement of the intercalated SRSR(61,2) (-)-(7S,8R,9S,1 0R)-N6-[10-(7,8,9,10- tetrahydrobenzo[a]pyrenyl)]-2'-deoxyadenosyl adduct from 1H NMR Authors: Zegar, I.S. / Kim, S.J. / Johansen, T.N. / Horton, P.J. / Harris, C.M. / Harris, T.M. / Stone, M.P. #1: Journal: Chem.Res.Toxicol. / Year: 1995 Title: Solution Structure of an Oligodeoxynucleotide Containing the Human N-Ras Codon 61 Sequence Refined from 1H NMR Using Molecular Dynamics Restrained by Nuclear Overhauser Effects Authors: Feng, B. / Stone, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1agu.cif.gz | 26.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1agu.ent.gz | 17.2 KB | Display | PDB format |
PDBx/mmJSON format | 1agu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1agu ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1agu | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 3718.586 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C10R-BPDE-N6-ADENINE ADDUCT |
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#2: DNA chain | Mass: 3291.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: C10R-BPDE-N6-ADENINE ADDUCT |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Sample conditions | pH: 6.9 / Temperature: 293 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer | Type: Bruker AMX500 / Manufacturer: Bruker / Model: AMX500 / Field strength: 500 MHz |
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-Processing
Software |
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NMR software |
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Refinement | Method: NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: THIS STRUCTURE PROVIDED THE BEST-FIT FOR THE NOE DATA BASED ON THE RELAXATION MATRIX ANALYSIS USING CORMA. Conformers calculated total number: 1 / Conformers submitted total number: 1 |