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- PDB-4fex: Crystal structure of the aminoglycoside phosphotransferase APH(3'... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4fex | ||||||
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Title | Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor tyrphostin AG1478 | ||||||
![]() | Aminoglycoside 3'-phosphotransferase AphA1-IAB | ||||||
![]() | transferase/transferase INHIBITOR / tyrphostin / 4-anilinoquinazoline / tyrphostin AG1478 / AG1478 / protein kinase inhibitor / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / EUKARYOTIC PROTEIN KINASE-LIKE FOLD / ALPHA/BETA PROTEIN / TRANSFERASE / PHOSPHOTRANSFERASE / AMINOGLYCOSIDE PHOSPHOTRANSFERASE / ANTIBIOTIC RESISTANCE / AMINOGLYCOSIDES / KANAMYCIN / GTP / INTRACELLULAR / transferase-transferase INHIBITOR complex | ||||||
Function / homology | ![]() kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Minasov, G. / Egorova, O. / Di Leo, R. / Shakya, T. / Spanogiannopoulos, P. / Wright, G.D. / Savchenko, A. ...Stogios, P.J. / Evdokimova, E. / Wawrzak, Z. / Minasov, G. / Egorova, O. / Di Leo, R. / Shakya, T. / Spanogiannopoulos, P. / Wright, G.D. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance. Authors: Stogios, P.J. / Spanogiannopoulos, P. / Evdokimova, E. / Egorova, O. / Shakya, T. / Todorovic, N. / Capretta, A. / Wright, G.D. / Savchenko, 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 | ![]() | 276.9 KB | Display | ![]() |
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PDB format | ![]() | 225 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 52.5 KB | Display | |
Data in CIF | ![]() | 68.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ej7SC ![]() 4feuC ![]() 4fevC ![]() 4fewC ![]() 4gkhC ![]() 4gkiC S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 31022.139 Da / Num. of mol.: 5 / Fragment: APHA1-IAB Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 186 molecules ![](data/chem/img/KAN.gif)
![](data/chem/img/0TO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/0TO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-KAN / #3: Chemical | ChemComp-0TO / #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.03 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 2.5 Details: 0.1 M sodium acetate pH 4.5, 14% PEG3350, 0.3 M NDSB221, 2% DMSO, 2 mM kanamycin, 5 mM tyrphostin AG1478, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2011 / Details: BERYLLIUM LENSES |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→20 Å / Num. obs: 45480 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 3.9 % / Rsym value: 0.061 / Net I/σ(I): 19.39 |
Reflection shell | Resolution: 2.71→2.76 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.043 / Num. unique all: 2305 / Rsym value: 0.562 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4EJ7 Resolution: 2.71→19.901 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.86 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.46 Å2 / ksol: 0.302 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.71→19.901 Å
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Refine LS restraints |
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LS refinement shell |
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