+Open data
-Basic information
Entry | Database: PDB / ID: 193d | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SOLUTION STRUCTURE OF A QUINOMYCIN BISINTERCALATOR-DNA COMPLEX | |||||||||
Components |
| |||||||||
Keywords | DNA/ANTIBIOTIC / BISINTERCALATOR / DEPSIPEPTIDE / QUINOXALINE / THIOACETAL / ANTIBIOTIC / ANTITUMOR / DNA-ANTIBIOTIC COMPLEX | |||||||||
Function / homology | uk63052 / 3-HYDROXYQUINALDIC ACID / DNA Function and homology information | |||||||||
Biological species | STREPTOMYCES (bacteria) | |||||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS, MATRIX RELAXATION | |||||||||
Authors | Chen, H. / Patel, D.J. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1995 Title: Solution Structure of a Quinomycin Bisintercalator-DNA Complex. Authors: Chen, H. / Patel, D.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 193d.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb193d.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 193d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 193d_validation.pdf.gz | 377 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 193d_full_validation.pdf.gz | 419.1 KB | Display | |
Data in XML | 193d_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 193d_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/93/193d ftp://data.pdbj.org/pub/pdb/validation_reports/93/193d | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Atom site foot note | 1: ALA D 2 - CYS D 3 MODEL 1 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 2: ALA C 2 - CYS C 3 MODEL 2 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 3: ALA D 2 - CYS D 3 MODEL 3 OMEGA = 0.00 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 4: ALA D 2 - CYS D 3 MODEL 4 OMEGA = 359.98 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 7: SER C 1 IS A D-SERINE. / 8: SER D 1 IS A D-SERINE. | |||||||||
NMR ensembles |
|
-Components
#1: DNA chain | Mass: 2426.617 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESIZED #2: Protein/peptide | | #3: Chemical | Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 189.167 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H7NO3 Details: QUINOMYCIN UK63052 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 HYDROXYQUINOXALINE ...Details: QUINOMYCIN UK63052 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 HYDROXYQUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5. References: uk63052 Compound details | QUINOMYCIN UK63052 IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...QUINOMYCIN | |
---|
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
---|
-Sample preparation
Details | Solvent system: D2O |
---|---|
Crystal grow | *PLUS Method: other / Details: NMR |
-Processing
Software |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
NMR software | Name: X-PLOR / Developer: BRUNGER / Classification: refinement | ||||||||
Refinement | Method: MOLECULAR DYNAMICS, MATRIX RELAXATION / Software ordinal: 1 Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A ...Details: TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE- RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 0.5 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 120 AND 180 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.023 0.024 0.024 0.026 BOND (ANG) 0.011 0.011 0.011 0.011 ANGLES (DEG) 3.616 3.657 3.700 3.725 IMPROPERS (DEG) 0.274 0.285 0.241 0.298 | ||||||||
NMR ensemble | Conformer selection criteria: all calculated structures submitted Conformers calculated total number: 4 / Conformers submitted total number: 4 |