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- PDB-4xdk: Crystal structure of human two pore domain potassium ion channel ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4xdk | ||||||
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Title | Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with norfluoxetine | ||||||
![]() | Potassium channel subfamily K member 10 | ||||||
![]() | TRANSPORT PROTEIN / OUTWARD RECTIFICATION / MEMBRANE PROTEIN / K2P / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | ![]() TWIK related potassium channel (TREK) / Phase 4 - resting membrane potential / stabilization of membrane potential / potassium ion leak channel activity / outward rectifier potassium channel activity / monoatomic ion channel complex / potassium channel activity / potassium ion transmembrane transport / memory / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pike, A.C.W. / Dong, Y.Y. / Mackenzie, A. / Mukhopadhyay, S. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
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![]() | ![]() Title: K2P channel gating mechanisms revealed by structures of TREK-2 and a complex with Prozac. Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, ...Authors: Dong, Y.Y. / Pike, A.C. / Mackenzie, A. / McClenaghan, C. / Aryal, P. / Dong, L. / Quigley, A. / Grieben, M. / Goubin, S. / Mukhopadhyay, S. / Ruda, G.F. / Clausen, M.V. / Cao, L. / Brennan, P.E. / Burgess-Brown, N.A. / Sansom, M.S. / Tucker, S.J. / Carpenter, E.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 386 KB | Display | ![]() |
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PDB format | ![]() | 314.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 33.3 KB | Display | |
Data in CIF | ![]() | 45.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bw5C ![]() 4xdjSC ![]() 4xdlC 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 31060.111 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 67-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-K / #3: Chemical | ChemComp-PC1 / #4: Chemical | ChemComp-408 / ( #5: Chemical | ChemComp-405 / ( |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 68.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M KCl, 0.2M ammonium formate, 0.1M Tris pH 7, 31% pentaerythritol ethoxylate 15/04 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→39.87 Å / Num. obs: 21872 / % possible obs: 99.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 135.63 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 3.6→3.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.808 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4xdj Resolution: 3.6→39.87 Å / Cor.coef. Fo:Fc: 0.8857 / Cor.coef. Fo:Fc free: 0.8886 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.498
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Displacement parameters | Biso mean: 181.6 Å2
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Refine analyze | Luzzati coordinate error obs: 1.109 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.6→39.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.6→3.78 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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