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Yorodumi- PDB-2k4l: Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k4l | ||||||||||||||||||
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Title | Solution structure of a 2:1C2-(2-naphthyl)pyrrolo[2,1-c][1,4]benzodiazepine (PBD) DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. | ||||||||||||||||||
Components | 5'-D(*Keywords | DNA / pyrrolo[2 / 1-c][1 / 4]benzodiazepine / PBD / DNA Adduct | Function / homology | Chem-PZD / DNA / DNA (> 10) | Function and homology information Method | SOLUTION NMR / simulated annealing | Authors | Antonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M. | Citation | Journal: Biochemistry / Year: 2008 Title: Solution structure of a 2:1 C2-(2-naphthyl) pyrrolo[2,1-c][1,4]benzodiazepine DNA adduct: molecular basis for unexpectedly high DNA helix stabilization. Authors: Antonow, D. / Barata, T. / Jenkins, T.C. / Parkinson, G.N. / Howard, P.W. / Thurston, D.E. / Zloh, M. #1: Journal: J.Comb.Chem. / Year: 2007 Title: Parallel Synthesis of a Novel C2-Aryl Pyrrolo[2,1-c][1,4]benzodiazepine (PBD) Library Authors: Antonow, D. / Cooper, N. / Howard, P.W. / Thurston, D.E. History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k4l.cif.gz | 200.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k4l.ent.gz | 165.9 KB | Display | PDB format |
PDBx/mmJSON format | 2k4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k4l_validation.pdf.gz | 458.4 KB | Display | wwPDB validaton report |
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Full document | 2k4l_full_validation.pdf.gz | 518.1 KB | Display | |
Data in XML | 2k4l_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2k4l_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k4/2k4l ftp://data.pdbj.org/pub/pdb/validation_reports/k4/2k4l | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: DNA chain | Mass: 4277.827 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE ...Details: THE 14-MER NUCLEOTIDE SEQUENCE AATCTTTAAAGATT WAS SYNTHESISED USING AN APPLIED BIOSYSTEMS DNA SYNTHESIZER. THE DNA SEQUENCE WAS PURIFIED BY REVERSED-PHASE HPLC AT ROOM TEMPERATURE. THE DUPLEX WAS FORMED BY ANNEALING IN PHOSPHATE BUFFER. #2: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.68 mM DNA (5'-D(*(DA)P*(DA)P*(DT)P*(DC)P*(DT)P*(DT)P*(DT)P*(DA)P*(DA)P*(DA)P*(DG)P*(DA)P*(DT)P*(DT))-3'), 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.68 mM / Component: DNA |
Sample conditions | Ionic strength: 130 / pH: 6.85 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE ...Details: DISTANCES RESTRAINTS WERE CALCULATED FROM THREE-DIMENSIONAL NOESY PEAK VOLUMES BY COMPARING TO REFERENCE VOLUME OF CYTOSINE (2.45 A BETWEEN H5 AND H6). ALL DISTANCE CONSTRAINTS WERE CLASSIFIED ACCORDING TO CROSSPEAK INTENSITIES AS (S) STRONG (1.80 TO 2.90), (M) MEDIUM (1.80 TO 4.00) AND (W) WEAK (D = 4.0, -2.2/+1.0 ). DISTANCE CONSTRAINS WITH METHYL PROTONS WERE CONSIDERED SEPARATELY (D = 4.0 , -2.2/+1.5 ). THE SIMULATED ANNEALING APPROACH WAS USED TO GENERATE 200 STRUCTURES. THE 10 LOWEST ENERGY STRUCTURES WERE CHOSEN AND THE ROOT MEAN SQUARE DEVIATION VALUES CALCULATED. | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 374 / NOE intraresidue total count: 174 / NOE long range total count: 40 / NOE medium range total count: 18 / NOE sequential total count: 102 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å | ||||||||||||||||||||||||
NMR ensemble rms | Distance rms dev: 0 Å / Distance rms dev error: 0 Å |