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- PDB-5i2k: Structure of the human GluN1/GluN2A LBD in complex with 7-{[ethyl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5i2k | ||||||
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Title | Structure of the human GluN1/GluN2A LBD in complex with 7-{[ethyl(4-fluorophenyl)amino]methyl}-N,2-dimethyl-5-oxo-5H-[1,3]thiazolo[3,2-a]pyrimidine-3-carboxamide (compound 19) | ||||||
![]() | (Glutamate receptor ionotropic, NMDA ...) x 2 | ||||||
![]() | TRANSPORT PROTEIN / GluN1 / GluN2A / receptor / NMDA | ||||||
Function / homology | ![]() excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / glutamate receptor signaling pathway / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / glycine binding / positive regulation of calcium ion transport into cytosol / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / startle response / regulation of neuronal synaptic plasticity / monoatomic cation transmembrane transport / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / ligand-gated monoatomic ion channel activity / excitatory synapse / calcium ion homeostasis / synaptic cleft / MECP2 regulates neuronal receptors and channels / glutamate-gated calcium ion channel activity / sensory perception of pain / EPHB-mediated forward signaling / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / ionotropic glutamate receptor signaling pathway / neurogenesis / positive regulation of synaptic transmission, glutamatergic / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / postsynaptic density membrane / visual learning / cytoplasmic vesicle membrane / protein catabolic process / brain development / regulation of synaptic plasticity / negative regulation of protein catabolic process / terminal bouton / memory / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / postsynaptic membrane / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / glutamatergic synapse / synapse / dendrite / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wallweber, H.J.A. / Lupardus, P.J. | ||||||
![]() | ![]() Title: Discovery of GluN2A-Selective NMDA Receptor Positive Allosteric Modulators (PAMs): Tuning Deactivation Kinetics via Structure-Based Design. Authors: Volgraf, M. / Sellers, B.D. / Jiang, Y. / Wu, G. / Ly, C.Q. / Villemure, E. / Pastor, R.M. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Sun, L. / Fu, Y. / Lupardus, P.J. / ...Authors: Volgraf, M. / Sellers, B.D. / Jiang, Y. / Wu, G. / Ly, C.Q. / Villemure, E. / Pastor, R.M. / Yuen, P.W. / Lu, A. / Luo, X. / Liu, M. / Zhang, S. / Sun, L. / Fu, Y. / Lupardus, P.J. / Wallweber, H.J. / Liederer, B.M. / Deshmukh, G. / Plise, E. / Tay, S. / Reynen, P. / Herrington, J. / Gustafson, A. / Liu, Y. / Dirksen, A. / Dietz, M.G. / Liu, Y. / Wang, T.M. / Hanson, J.E. / Hackos, D. / Scearce-Levie, K. / Schwarz, J.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.2 KB | Display | ![]() |
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PDB format | ![]() | 97.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5i2nC ![]() 5kdtC ![]() 2a5tS 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
-Glutamate receptor ionotropic, NMDA ... , 2 types, 2 molecules AB
#1: Protein | Mass: 31883.441 Da / Num. of mol.: 1 Fragment: UNP residues 401-539, GT linker, UNP residues 661-802 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 33409.074 Da / Num. of mol.: 1 Fragment: UNP residues 415-565, GT linker, UNP residues 684-821 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 58 molecules ![](data/chem/img/GLU.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/67H.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GLY.gif)
![](data/chem/img/67H.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GLU / |
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#4: Chemical | ChemComp-GLY / |
#5: Chemical | ChemComp-67H / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 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: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2013 |
Radiation | Monochromator: asymmetric curved crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.86→119 Å / Num. obs: 14323 / % possible obs: 99.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 71.23 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 2.86→3.01 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.479 / Mean I/σ(I) obs: 3.4 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2A5T Resolution: 2.86→59.72 Å / Cor.coef. Fo:Fc: 0.9324 / Cor.coef. Fo:Fc free: 0.8795 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.408
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Displacement parameters | Biso mean: 51.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.292 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.86→59.72 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.86→3.09 Å / Total num. of bins used: 7
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