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- PDB-2oey: Solution Structure of a Designed Spirocyclic Helical Ligand Bindi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oey | ||||||
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Title | Solution Structure of a Designed Spirocyclic Helical Ligand Binding at a Two-Base Bulge Site in DNA | ||||||
![]() | DNA (25-MER) | ||||||
![]() | DNA / Designed spirocyclic helical ligand-bulged DNA complex | ||||||
Function / homology | Chem-S2A / DNA / DNA (> 10)![]() | ||||||
Method | SOLUTION NMR / simulated annealing, molecular dynamics | ||||||
![]() | Zhang, N. / Lin, Y. / Xiao, Z. / Jones, G.B. / Goldberg, I.H. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150 KB | Display | ![]() |
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PDB format | ![]() | 118.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.6 KB | Display | ![]() |
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Full document | ![]() | 476.8 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 18.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: DNA chain | Mass: 7680.945 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This is an artifical sequence |
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#2: Chemical | ChemComp-S2A / ( |
-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 methods for DNA-drug complex. |
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Sample preparation
Details |
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Sample conditions |
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-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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Processing
NMR software |
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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 |