[English] 日本語
Yorodumi- PDB-2oey: Solution Structure of a Designed Spirocyclic Helical Ligand Bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oey | ||||||
---|---|---|---|---|---|---|---|
Title | Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA | ||||||
Components | DNA (25-MER) | ||||||
Keywords | DNA / Designed spirocyclic helical ligand-bulged DNA complex | ||||||
Function / homology | Chem-S2A / DNA / DNA (> 10) Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
Authors | Zhang, N. / Lin, Y. / Xiao, Z. / Jones, G.B. / Goldberg, I.H. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA. Authors: Zhang, N. / Lin, Y. / Xiao, Z. / Jones, G.B. / Goldberg, I.H. #1: Journal: Science / Year: 1996 Title: Solution structure of a two-base DNA bulge complexed with an enediyne cleaving analogue Authors: Stassinopoulos, A. / Ji, J. / Gao, X. / Goldberg, I.H. #2: Journal: Biochemistry / Year: 2002 Title: Induced formation of a DNA bulge structure by a molecular wedge ligand-post activated neocarzinostatin chromophore Authors: Gao, X. / Stassinopolous, A. / Ji, J. / Kwon, Y. / Bare, S. / Goldberg, I.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2oey.cif.gz | 150 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2oey.ent.gz | 118.3 KB | Display | PDB format |
PDBx/mmJSON format | 2oey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oey_validation.pdf.gz | 425.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2oey_full_validation.pdf.gz | 476.8 KB | Display | |
Data in XML | 2oey_validation.xml.gz | 12.8 KB | Display | |
Data in CIF | 2oey_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oey ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oey | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 7680.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This is an artifical sequence |
---|---|
#2: Chemical | ChemComp-S2A / ( |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||
NMR details | Text: This structure was determined using standard methods for DNA-drug complex. |
-Sample preparation
Details |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
|
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
---|---|
Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: simulated annealing, molecular dynamics / Software ordinal: 1 Details: the structures are based on a total of 531 restraints, 506 are NOE-derived distance constraints, 25 dihedral angle restraints,40 distance restraints from hydrogen bonds. | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: back calculated data agree with experimental NOESY spectrum Conformers calculated total number: 10 / Conformers submitted total number: 8 |