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Open data
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Basic information
Entry | Database: PDB / ID: 1xvn | ||||||
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Title | echinomycin (ACGTACGT)2 complex | ||||||
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![]() | DNA/ANTIBIOTIC / BISINTERCALATOR / HOOGSTEEN BASEPAIR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX | ||||||
Function / homology | Echinomycin / 2-CARBOXYQUINOXALINE / : / DNA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cuesta-Seijo, J.A. / Sheldrick, G.M. | ||||||
![]() | ![]() Title: Structures of Complexes between Echinomycin and Duplex DNA. Authors: Cuesta-Seijo, J.A. / Sheldrick, G.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 27.8 KB | Display | ![]() |
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PDB format | ![]() | 20.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 418 KB | Display | ![]() |
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Full document | ![]() | 419.3 KB | Display | |
Data in XML | ![]() | 4.5 KB | Display | |
Data in CIF | ![]() | 5.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||||
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#2: Protein/peptide | ![]() Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. Source: (natural) ![]() | ||||
#3: Chemical | ChemComp-MG / | ||||
#4: Chemical | ![]() Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. References: Echinomycin #5: Water | ChemComp-HOH / | Compound details | THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...THE ECHINOMYCI | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.32 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 Details: PEG 200, PEG 3350, MGCL2, MES, SPERMINE-HCL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 11, 2003 |
Radiation | Monochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→26.2 Å / Num. obs: 6499 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 21.27 % / Rmerge(I) obs: 0.0424 / Rsym value: 0.0424 / Net I/σ(I): 39.11 |
Reflection shell | Resolution: 1.5→1.6 Å / Redundancy: 20.44 % / Rmerge(I) obs: 0.4225 / Mean I/σ(I) obs: 9.03 / Rsym value: 0.4225 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: THE SKELETON OF ECHINOMYCIN IS NEARLY SYMMETRIC (NOT MODELLED TO DO SO), THE BRIDGE IS NOT. BOTH POSSIBLE ORIENTATIONS OF BINDING WERE OBSERVED AND ARE MODELLED AS DISORDERED/MICROHETE.
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Refine analyze | Num. disordered residues: 7 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→26.2 Å
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