+
Open data
-
Basic information
Entry | Database: PDB / ID: 1xvr | ||||||
---|---|---|---|---|---|---|---|
Title | echinomycin (CGTACG)2 complex | ||||||
![]() |
| ||||||
![]() | 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 34.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 26.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 436.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 441.6 KB | Display | |
Data in XML | ![]() | 5.3 KB | Display | |
Data in CIF | ![]() | 6.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 1809.217 Da / Num. of mol.: 2 / Source method: obtained synthetically #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 | #4: Chemical | ChemComp-QUI / ![]() 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: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.32 % | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6 Details: MPD, MGCL2, MES, SPERMINE-HCL, PH 6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 285K | ||||||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 1.4→16.5 Å / Num. obs: 10857 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 3.82 % / Rmerge(I) obs: 0.0546 / Rsym value: 0.0546 / Net I/σ(I): 12.72 |
Reflection shell | Resolution: 1.4→1.5 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.275 / Mean I/σ(I) obs: 4.87 / Rsym value: 0.275 / % possible all: 94.3 |
-
Processing
Software |
| ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||
Refine analyze | Num. disordered residues: 4 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→16.5 Å
|