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- PDB-5ewm: CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ewm | |||||||||
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Title | CRYSTAL STRUCTURE OF AMINO TERMINAL DOMAINS OF THE NMDA RECEPTOR SUBUNIT GLUN1 AND GLUN2B IN COMPLEX WITH EVT-101 | |||||||||
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![]() | TRANSPORT PROTEIN / Glutamate receptor / allosteric modulator / GluN2B antagonists | |||||||||
Function / homology | ![]() excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / positive regulation of cysteine-type endopeptidase activity / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins ...excitatory chemical synaptic transmission / Activated NTRK2 signals through FYN / Synaptic adhesion-like molecules / positive regulation of cysteine-type endopeptidase activity / negative regulation of dendritic spine maintenance / regulation of monoatomic cation transmembrane transport / glutamate receptor signaling pathway / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / glycine binding / response to zinc ion / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / positive regulation of excitatory postsynaptic potential / Long-term potentiation / MECP2 regulates neuronal receptors and channels / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / EPHB-mediated forward signaling / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / long-term synaptic potentiation / postsynaptic density membrane / regulation of synaptic plasticity / brain development / late endosome / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / postsynaptic membrane / response to ethanol / postsynaptic density / learning or memory / lysosome / cytoskeleton / neuron projection / endoplasmic reticulum membrane / cell surface / zinc ion binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Pandit, J. | |||||||||
![]() | ![]() Title: A Novel Binding Mode Reveals Two Distinct Classes of NMDA Receptor GluN2B-selective Antagonists. Authors: Stroebel, D. / Buhl, D.L. / Knafels, J.D. / Chanda, P.K. / Green, M. / Sciabola, S. / Mony, L. / Paoletti, P. / Pandit, 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 | ![]() | 582.8 KB | Display | ![]() |
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PDB format | ![]() | 479.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 52.8 KB | Display | |
Data in CIF | ![]() | 73.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ewjSC ![]() 5ewlC 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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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules ACBD
#1: Protein | Mass: 43757.977 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 23-408) / Mutation: N61Q,N371Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 41351.902 Da / Num. of mol.: 2 / Fragment: Amino Terminal Domain (UNP residues 31-394) / Mutation: N348D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 7 molecules ![](data/chem/img/NAG.gif)
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 297 molecules ![](data/chem/img/NA.gif)
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#4: Chemical | ChemComp-NA / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 3.6M Na Formate, 0.1 M Hepes pH 7.0 / PH range: 6.8-7.2 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2014 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.76→129.57 Å / Num. obs: 53496 / % possible obs: 98.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 77.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.036 / Net I/σ(I): 14.1 / Num. measured all: 177662 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5EWJ Resolution: 2.76→40.41 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9208 / SU R Cruickshank DPI: 0.602 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.577 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.272
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Displacement parameters | Biso mean: 77.45 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→40.41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.76→2.83 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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