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- PDB-4xnx: X-ray structure of Drosophila dopamine transporter in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xnx | |||||||||
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Title | X-ray structure of Drosophila dopamine transporter in complex with reboxetine | |||||||||
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![]() | transport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / transport protein-inhibitor complex | |||||||||
Function / homology | ![]() Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / cocaine binding / dopamine:sodium symporter activity / norepinephrine:sodium symporter activity / norepinephrine transport / response to odorant / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / dopamine uptake involved in synaptic transmission / amino acid transport / neuronal cell body membrane / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / neuron projection / axon / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Aravind, P. / Wang, K. / Gouaux, E. | |||||||||
![]() | ![]() Title: X-ray structures of Drosophila dopamine transporter in complex with nisoxetine and reboxetine. Authors: Penmatsa, A. / Wang, K.H. / Gouaux, E. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 207.1 KB | Display | ![]() |
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PDB format | ![]() | 158.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 49.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xnuC ![]() 4m48S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 2 molecules LH
#2: Antibody | Mass: 23306.586 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 25921.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 60148.539 Da / Num. of mol.: 1 / Mutation: V74, L415A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Polysaccharide | alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose |
-Non-polymers , 5 types, 12 molecules ![](data/chem/img/CLR.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/41X.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/41X.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / | #8: Chemical | ChemComp-41X / ( | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.92 Å3/Da / Density % sol: 75.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 350 MME 38%, Glycine 0.1M / PH range: 9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.997→48.417 Å / Num. obs: 46863 / % possible obs: 99.4 % / Redundancy: 14.4 % / Biso Wilson estimate: 116.6 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 14 % / Rmerge(I) obs: 0.866 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M48 Resolution: 3→48.42 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.6 / Stereochemistry target values: ML Details: Residue H CYS 134 and Residue H THR 138 are not properly linked: distance between C and N is 9.24.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 110.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.42 Å
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Refine LS restraints |
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LS refinement shell |
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