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- PDB-6m3z: X-ray structure of a Drosophila dopamine transporter with NET-lik... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6m3z | |||||||||
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Title | X-ray structure of a Drosophila dopamine transporter with NET-like mutations (D121G/S426M/F471L) in milnacipran bound form | |||||||||
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![]() | MEMBRANE PROTEIN / neurotransmitter transporter / antibody fragment | |||||||||
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 | ![]() ![]() ![]() | |||||||||
![]() | Shabareesh, P. / Mallela, A.K. / Joseph, D. / Penmatsa, A. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of norepinephrine recognition and transport inhibition in neurotransmitter transporters. Authors: Pidathala, S. / Mallela, A.K. / Joseph, D. / Penmatsa, 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 | ![]() | 211.1 KB | Display | ![]() |
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PDB format | ![]() | 161.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 49.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6m0fC ![]() 6m0zC ![]() 6m2rC ![]() 6m38C ![]() 6m47C ![]() 4xnxS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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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: 23619.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 60100.602 Da / Num. of mol.: 1 / Mutation: V74A,D121G,L415A,S426M,F471L,Deletion 162-202 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#4: Polysaccharide |
-Non-polymers , 8 types, 28 molecules ![](data/chem/img/F0F.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/Y01.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/D10.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/Y01.gif)
![](data/chem/img/CLR.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-F0F / ( | ||||||
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#6: Chemical | ChemComp-GOL / | ||||||
#7: Chemical | ChemComp-D10 / | ||||||
#8: Chemical | ChemComp-CL / | ||||||
#9: Chemical | #10: Chemical | ChemComp-Y01 / | #11: Chemical | ChemComp-CLR / | #12: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.41 Å3/Da / Density % sol: 77.27 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M MOPS pH 7.0, 32 PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.106→48.552 Å / Num. obs: 42441 / % possible obs: 99.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 97.11 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.079 / Rrim(I) all: 0.185 / Net I/σ(I): 6.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4xnx Resolution: 3.11→48.55 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.78 / 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: 148.19 Å2 / Biso mean: 84.6215 Å2 / Biso min: 55.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.11→48.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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