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Open data
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Basic information
Entry | Database: PDB / ID: 1vtg | ||||||
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Title | THE MOLECULAR STRUCTURE OF A DNA-TRIOSTIN A COMPLEX | ||||||
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![]() | DNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX | ||||||
Function / homology | TRIOSTIN A / 2-CARBOXYQUINOXALINE / : / DNA![]() | ||||||
Biological species | synthetic construct (others)![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, A.H.-J. / Ughetto, G. / Quigley, G.J. / Hakoshima, T. / Van Der Marel, G.A. / Van Boom, J.H. / Rich, A. | ||||||
![]() | ![]() Title: The molecular structure of a DNA-triostin A complex. Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Hakoshima, T. / van der Marel, G.A. / van Boom, J.H. / Rich, A. #1: Journal: Nucleic Acids Res. / Year: 1985 Title: A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. Authors: Ughetto, G. / Wang, A.H. / Quigley, G.J. / van der Marel, G.A. / van Boom, J.H. / Rich, A. #2: ![]() Title: Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin A-d(GCGTACGC) complex. Authors: Wang, A.H. / Ughetto, G. / Quigley, G.J. / Rich, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 17.2 KB | Display | ![]() |
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PDB format | ![]() | 10.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 367.8 KB | Display | ![]() |
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Full document | ![]() | 381.8 KB | Display | |
Data in XML | ![]() | 4.6 KB | Display | |
Data in CIF | ![]() | 5.2 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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1 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||
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#2: Protein/peptide | ![]() Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. Source: (synth.) ![]() | ||
#3: Chemical | ![]() Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE ...Details: TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A DISULPHIDE BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. References: TRIOSTIN A Compound details | TRIOSTIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ...TRIOSTIN IS A BICYCLIC OCTADEPSIP | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.28 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 7 / Details: pH 7.00, VAPOR DIFFUSION | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 257 K |
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Detector | Type: NICOLET P3 / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Num. obs: 2995 / Observed criterion σ(I): 1 |
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Processing
Software | Name: NUCLSQ / Classification: refinement | ||||||||||||
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Refinement | Rfactor obs: 0.189 / Highest resolution: 1.67 Å Details: COORDINATES ARE REPORTED IN THE JRNL REFERENCE PAPER AS A COMPARISON. | ||||||||||||
Refine Biso | Class: ALL ATOMS / Details: TR / Treatment: isotropic | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.67 Å
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