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Open data
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Basic information
Entry | Database: PDB / ID: 5h8s | ||||||
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Title | Structure of the human GluA2 LBD in complex with GNE3419 | ||||||
![]() | Glutamate receptor 2,Glutamate receptor 2 | ||||||
![]() | TRANSPORT PROTEIN / GluN1 / GluN2A / NMDA / receptor | ||||||
Function / homology | ![]() Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Long-term potentiation / AMPA glutamate receptor complex / excitatory synapse / asymmetric synapse ...Activation of AMPA receptors / postsynaptic endocytic zone / Trafficking of GluR2-containing AMPA receptors / Unblocking of NMDA receptors, glutamate binding and activation / AMPA glutamate receptor activity / ligand-gated monoatomic cation channel activity / Long-term potentiation / AMPA glutamate receptor complex / excitatory synapse / asymmetric synapse / MECP2 regulates neuronal receptors and channels / glutamate-gated receptor activity / ionotropic glutamate receptor signaling pathway / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / postsynaptic density membrane / modulation of chemical synaptic transmission / endocytic vesicle membrane / amyloid-beta binding / chemical synaptic transmission / postsynapse / dendritic spine / postsynaptic density / external side of plasma membrane / neuronal cell body / dendrite / signal transduction / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wallweber, H.J.A. / Lupardus, P.J. | ||||||
![]() | ![]() Title: Positive Allosteric Modulators of GluN2A-Containing NMDARs with Distinct Modes of Action and Impacts on Circuit Function. Authors: Hackos, D.H. / Lupardus, P.J. / Grand, T. / Chen, Y. / Wang, T.M. / Reynen, P. / Gustafson, A. / Wallweber, H.J. / Volgraf, M. / Sellers, B.D. / Schwarz, J.B. / Paoletti, P. / Sheng, M. / Zhou, Q. / Hanson, J.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 183.8 KB | Display | ![]() |
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PDB format | ![]() | 145.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5h8fC ![]() 5h8hC ![]() 5h8nC ![]() 5h8qC ![]() 5kcjC ![]() 1ftjS 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
-Protein , 1 types, 3 molecules ACB
#1: Protein | Mass: 29210.662 Da / Num. of mol.: 3 Fragment: UNP residues 413-527, GT linker, UNP residues 653-796 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 678 molecules ![](data/chem/img/GLU.gif)
![](data/chem/img/5YC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5YC.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CAC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CAC / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1:2 v/v protein to mother liquor (0.1 M HEPES, pH 7.0, 10-13% PEG8000, 2 mM calcium acetate) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 5, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 96862 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 23.6 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1FTJ Resolution: 1.703→46.812 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.87 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.703→46.812 Å
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Refine LS restraints |
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LS refinement shell |
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