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- PDB-4xpb: X-ray structure of Drosophila dopamine transporter with subsiteB ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xpb | |||||||||
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Title | X-ray structure of Drosophila dopamine transporter with subsiteB mutations (D121G/S426M) bound to cocaine | |||||||||
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![]() | tranport protein/inhibitor / integral membrane protein / all-alpha helical antidepressant complex / tranport 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 / axon / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Aravind, P. / Wang, K. / Gouaux, E. | |||||||||
![]() | ![]() Title: Neurotransmitter and psychostimulant recognition by the dopamine transporter. Authors: Wang, K.H. / Penmatsa, A. / 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 | ![]() | 199 KB | Display | ![]() |
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PDB format | ![]() | 156.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 35.8 KB | Display | |
Data in CIF | ![]() | 48.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xp1C ![]() 4xp4C ![]() 4xp5C ![]() 4xp6C ![]() 4xp9C ![]() 4xpaC ![]() 4xpfC ![]() 4xpgC ![]() 4xphC ![]() 4xptC 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: 60925.605 Da / Num. of mol.: 1 / Mutation: V74A, D121G, S426M 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, 8 molecules ![](data/chem/img/NA.gif)
![](data/chem/img/COC.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/COC.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | #6: Chemical | ChemComp-COC / | #7: Chemical | #8: Chemical | ChemComp-CL / | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.36 Å3/Da / Density % sol: 77.06 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 400 (38%), Tris-Bicine 0.1M / PH range: pH 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 16, 2013 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. obs: 41179 / % possible obs: 93 % / Redundancy: 4.6 % / Biso Wilson estimate: 111.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.879 / % possible all: 94.5 |
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Processing
Software |
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Refinement | Resolution: 3.05→48.33 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.3 / 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 mean: 109.5 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.05→48.33 Å
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