[English] 日本語
![](img/lk-miru.gif)
- PDB-4gee: Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4gee | ||||||
---|---|---|---|---|---|---|---|
Title | Pyrrolopyrimidine inhibitors of DNA gyrase B and topoisomerase IV, part I: structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. | ||||||
![]() | DNA gyrase subunit B | ||||||
![]() | Isomerase/Isomerase inhibitor / ATP-binding / Nucleotide-binding / Topoisomerase / ATP-binding domain / DNA gyrase negatively supercoils closed circular double-stranded DNA in an ATP-dependent manner and also catalyzes the interconversion of other topological isomers of double-stranded DNA rings / Isomerase-Isomerase inhibitor complex | ||||||
Function / homology | ![]() DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bensen, D.C. / Chen, Z. / Tari, L.W. | ||||||
![]() | ![]() Title: Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV (ParE). Part I: Structure guided discovery and optimization of dual targeting agents with potent, broad-spectrum enzymatic activity. Authors: Tari, L.W. / Trzoss, M. / Bensen, D.C. / Li, X. / Chen, Z. / Lam, T. / Zhang, J. / Creighton, C.J. / Cunningham, M.L. / Kwan, B. / Stidham, M. / Shaw, K.J. / Lightstone, F.C. / Wong, S.E. / ...Authors: Tari, L.W. / Trzoss, M. / Bensen, D.C. / Li, X. / Chen, Z. / Lam, T. / Zhang, J. / Creighton, C.J. / Cunningham, M.L. / Kwan, B. / Stidham, M. / Shaw, K.J. / Lightstone, F.C. / Wong, S.E. / Nguyen, T.B. / Nix, J. / Finn, J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 58 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 740.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 741.4 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gfnC ![]() 4gglC ![]() 4hxwC ![]() 4hxzC ![]() 4hy1C ![]() 4hymC ![]() 4hypC ![]() 4hz0C ![]() 4hz5C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 23835.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-0WT / ( |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.52 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 25% (w/v) PEG 1500, 3% (v/v) t-butanol, 20% (w/v) glycerol, 20 mM citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: NOIR-1 / Detector: CCD / Date: Aug 1, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.7→34.19 Å / Num. all: 23876 / Num. obs: 23876 / % possible obs: 98.9 % |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3181 / Rsym value: 0.385 / % possible all: 98.9 |
-
Processing
Software | Name: REFMAC / Version: 5.6.0117 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.315 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→34.19 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
|