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- PDB-3p4w: Structure of desflurane bound to a pentameric ligand-gated ion ch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3p4w | ||||||
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Title | Structure of desflurane bound to a pentameric ligand-gated ion channel, GLIC | ||||||
![]() | Glr4197 protein | ||||||
![]() | MEMBRANE PROTEIN / TRANSPORT PROTEIN / transmembrane helices / ligand-gated ion channel | ||||||
Function / homology | ![]() sodium channel activity / extracellular ligand-gated monoatomic ion channel activity / potassium channel activity / transmembrane transporter complex / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nury, H. / Van Renterghem, C. / Weng, Y. / Tran, A. / Baaden, M. / Dufresne, V. / Changeux, J.P. / Sonner, J.M. / Delarue, M. / Corringer, P.J. | ||||||
![]() | ![]() Title: X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel Authors: Nury, H. / Van Renterghem, C. / Weng, Y. / Tran, A. / Baaden, M. / Dufresne, V. / Changeux, J.P. / Sonner, J.M. / Delarue, M. / Corringer, P.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 327.9 KB | Display | ![]() |
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PDB format | ![]() | 266.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
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Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 59.3 KB | Display | |
Data in CIF | ![]() | 76.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3p50C ![]() 3eamS 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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Unit cell |
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Components
#1: Protein | Mass: 36348.805 Da / Num. of mol.: 5 / Fragment: residues in UNP 44-359 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-LMT / #3: Chemical | ChemComp-DSF / ( #4: Chemical | ChemComp-PLC / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.148761 Å3/Da / Density % sol: 76.110756 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 28, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→25 Å / Num. obs: 59199 / % possible obs: 97.5 % / Redundancy: 2 % / Biso Wilson estimate: 69.86 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 3.2→3.37 Å / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3eam Resolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.8762 / Cor.coef. Fo:Fc free: 0.8629 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.84 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.645 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.312
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Displacement parameters | Biso max: 158.16 Å2 / Biso mean: 63.12 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.525 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.28 Å / Total num. of bins used: 20
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