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Yorodumi- PDB-1ag5: THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ag5 | |||||||||
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Title | THE SOLUTION STRUCTURE OF AN AFLATOXIN B1 EPOXIDE ADDUCT AT THE N7 POSITION OF GUANINE OPPOSITE AN ADENINE IN THE COMPLEMENTARY STRAND OF AN OLIGODEOXYNUCLEOTIDE DUPLEX, NMR, MINIMIZED AVERAGE STRUCTURE | |||||||||
Components |
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Keywords | DNA / AFLATOXIN B1 / N7-GUANINE ADDUCT / INTERCALATION / DNA DUPLEX / DEOXYRIBONUCLEIC ACID | |||||||||
Function / homology | 8,9-DIHYDRO-9-HYDROXY-AFLATOXIN B1 / DNA / DNA (> 10) Function and homology information | |||||||||
Biological species | synthetic construct (others) | |||||||||
Method | SOLUTION NMR / NOE-RESTRAINED MOLECULAR DYNAMICS, SIMULATED ANNEALING | |||||||||
Authors | Johnson, D.S. / Stone, M.P. | |||||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Refined solution structure of 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 opposite CpA in the complementary strand of an oligodeoxynucleotide duplex as determined by 1H NMR. Authors: Johnston, D.S. / 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 | 1ag5.cif.gz | 25.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ag5.ent.gz | 16.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ag5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ag5_validation.pdf.gz | 408.1 KB | Display | wwPDB validaton report |
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Full document | 1ag5_full_validation.pdf.gz | 416.9 KB | Display | |
Data in XML | 1ag5_validation.xml.gz | 3.1 KB | Display | |
Data in CIF | 1ag5_validation.cif.gz | 3.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1ag5 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1ag5 | HTTPS FTP |
-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: 2964.957 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 OPPOSITE CPA IN THE COMPLEMENTARY STRAND Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3438.259 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXYAFLATOXIN B1 OPPOSITE CPA IN THE COMPLEMENTARY STRAND Source: (synth.) synthetic construct (others) |
#3: Chemical | ChemComp-AFN / |
-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: 278 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 |