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- PDB-4iy5: Crystal structure of the glua2 ligand-binding domain (S1S2J-L483Y... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4iy5 | ||||||
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Title | Crystal structure of the glua2 ligand-binding domain (S1S2J-L483Y-N754S) in complex with glutamate and CX516 at 2.0 A resolution | ||||||
![]() | Glutamate receptor 2![]() | ||||||
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Function / homology | ![]() spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Krintel, C. / Frydenvang, K. / Harpsoe, K. / Gajhede, M. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Structural analysis of the positive AMPA receptor modulators CX516 and Me-CX516 in complex with the GluA2 ligand-binding domain Authors: Krintel, C. / Harpsoe, K. / Zachariassen, L.G. / Peters, D. / Frydenvang, K. / Pickering, D.S. / Gajhede, M. / Kastrup, J.S. #1: ![]() Title: Thermodynamics and structural analysis of positive allosteric modulation of the ionotropic glutamate receptor GluA2. Authors: Krintel, C. / Frydenvang, K. / Olsen, L. / Kristensen, M.T. / de Barrios, O. / Naur, P. / Francotte, P. / Pirotte, B. / Gajhede, M. / Kastrup, J.S. #2: ![]() Title: Mechanism of positive allosteric modulators acting on AMPA receptors. Authors: Jin, R. / Clark, S. / Weeks, A.M. / Dudman, J.T. / Gouaux, E. / Partin, K.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 243.9 KB | Display | ![]() |
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PDB format | ![]() | 195.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4iy6C ![]() 3tdjS S: Starting model for refinement 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
-Protein , 1 types, 2 molecules AB
#1: Protein | ![]() Mass: 29244.678 Da / Num. of mol.: 2 Fragment: Ligand binding domain, UNP RESIDUES 413-527, 653-796 Mutation: L94Y, N242S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 586 molecules ![](data/chem/img/GLU.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CX5.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CX5.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ![]() #3: Chemical | ChemComp-SO4 / ![]() #4: Chemical | ![]() #5: Chemical | ![]() #6: Chemical | ChemComp-CX5 / | ![]() #7: Water | ChemComp-HOH / | ![]() |
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-Details
Sequence details | THE FUSION PROTEIN OF THE RESIDUES 413-527, LINKER GLY-THR, AND RESIDUES 653-796 FROM GLUA2 |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.54 % |
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Crystal grow![]() | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 24.4% PEG 4000, 0.3M lithium sulfate, 0.1M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 99 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 5, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→26.432 Å / Num. obs: 39394 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 3TDJ Resolution: 2→26.432 Å / SU ML: 0.18 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.49 / 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: 18.2 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→26.432 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Origin x: 29.3718 Å / Origin y: 16.8211 Å / Origin z: 3.3744 Å
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Refinement TLS group | Selection details: ALL |