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- PDB-4xnu: 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: 4xnu | ||||||
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Title | X-ray structure of Drosophila dopamine transporter in complex with nisoxetine | ||||||
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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 / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep ...Dopamine clearance from the synaptic cleft / Na+/Cl- dependent neurotransmitter transporters / circadian sleep/wake cycle / response to odorant / cocaine binding / norepinephrine transport / dopamine:sodium symporter activity / regulation of presynaptic cytosolic calcium ion concentration / dopamine transport / sleep / neuronal cell body membrane / dopamine uptake involved in synaptic transmission / amino acid transport / sodium ion transmembrane transport / adult locomotory behavior / presynaptic membrane / 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 | ![]() | 204.6 KB | Display | ![]() |
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PDB format | ![]() | 156.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 890.9 KB | Display | ![]() |
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Full document | ![]() | 905.4 KB | Display | |
Data in XML | ![]() | 34.7 KB | Display | |
Data in CIF | ![]() | 46.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xnxC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 59684.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 13 molecules 








#4: Chemical | #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-CLR / | #7: Chemical | ChemComp-41U / | #8: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 2.98→50 Å / Num. obs: 44010 / % possible obs: 99.4 % / Redundancy: 5.1 % / Biso Wilson estimate: 92.53 Å2 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.069 / Rrim(I) all: 0.137 / Χ2: 0.629 / Net I/av σ(I): 12.857 / Net I/σ(I): 3.9 / Num. measured all: 223836 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4M48 Resolution: 2.98→47.099 Å / FOM work R set: 0.7844 / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.21 / Stereochemistry target values: ML
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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 max: 177.48 Å2 / Biso mean: 85.68 Å2 / Biso min: 43.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.98→47.099 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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