[English] 日本語
![](img/lk-miru.gif)
- PDB-4xdl: Crystal structure of human two pore domain potassium ion channel ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xdl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human two pore domain potassium ion channel TREK2 (K2P10.1) in complex with a brominated fluoxetine derivative. | ||||||
![]() | 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 | ![]() ![]() ![]() | ||||||
![]() | Mackenzie, A. / Pike, A.C.W. / Dong, Y.Y. / Mukhopadhyay, S. / Ruda, G.F. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. ...Mackenzie, A. / Pike, A.C.W. / Dong, Y.Y. / Mukhopadhyay, S. / Ruda, G.F. / Brennan, P.E. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Burgess-Brown, N.A. / Carpenter, E.P. / Structural Genomics Consortium (SGC) | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 406.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 333.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 33.8 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4bw5C ![]() 4xdjSC ![]() 4xdkC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
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 | #5: Chemical | ChemComp-40D / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.75 Å3/Da / Density % sol: 67.23 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M KCl, 0.1M MES pH 6.5, 0.05M magnesium chloride, 0.001M cadmium chloride, 18% (v/v) PEG500 Dimethylether |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
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: 0.8856 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→39.07 Å / Num. obs: 24216 / % possible obs: 99.9 % / Redundancy: 11.4 % / Biso Wilson estimate: 122.95 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 11.2 % / Rmerge(I) obs: 1.846 / Mean I/σ(I) obs: 1.5 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4XDJ Resolution: 3.5→35 Å / Cor.coef. Fo:Fc: 0.8873 / Cor.coef. Fo:Fc free: 0.8842 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.499 Details: BOUND BR-FLUOXETINE LIGAND IS ONLY PARTIALLY RESOLVED IN ELECTRON DENSITY AND ONLY BROMINATED TRIFLUOROMETHYL PHENOXY PORTION HAS BEEN INCLUDED IN THE MODEL. OCCUPANCY OF BROMINE ATOM HAS ...Details: BOUND BR-FLUOXETINE LIGAND IS ONLY PARTIALLY RESOLVED IN ELECTRON DENSITY AND ONLY BROMINATED TRIFLUOROMETHYL PHENOXY PORTION HAS BEEN INCLUDED IN THE MODEL. OCCUPANCY OF BROMINE ATOM HAS BEEN REDUCED TO 0.8 TO ACCOUNT FOR EFFECTS OF RADIATION DAMAGE.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 157.05 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 1.023 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.5→35 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.65 Å / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|