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- PDB-5vii: Crystal structure of GluN1/GluN2A NMDA receptor agonist binding d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vii | |||||||||
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Title | Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 4-(3-fluoropropyl)phenyl-ACEPC | |||||||||
![]() | (Glutamate receptor ionotropic, NMDA ...) x 2 | |||||||||
![]() | TRANSPORT PROTEIN / RECEPTOR / NMDA receptor / Antagonist | |||||||||
Function / homology | ![]() neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned place preference / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / voltage-gated monoatomic cation channel activity / sleep / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / regulation of monoatomic cation transmembrane transport / cellular response to lipid / locomotion / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / regulation of NMDA receptor activity / glutamate-gated calcium ion channel activity / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / spinal cord development / dopamine metabolic process / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / monoatomic cation transport / regulation of neuronal synaptic plasticity / modulation of excitatory postsynaptic potential / response to lithium ion / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / response to light stimulus / positive regulation of protein targeting to membrane / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Mou, T.-C. / Conti, P. / Pinto, A. / Tamborini, L. / Sprang, S.R. / Hansen, K.B. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis of subunit selectivity for competitive NMDA receptor antagonists with preference for GluN2A over GluN2B subunits. Authors: Lind, G.E. / Mou, T.C. / Tamborini, L. / Pomper, M.G. / De Micheli, C. / Conti, P. / Pinto, A. / Hansen, K.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 | ![]() | 137.3 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 831.5 KB | Display | ![]() |
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Full document | ![]() | 839.8 KB | Display | |
Data in XML | ![]() | 27.3 KB | Display | |
Data in CIF | ![]() | 39.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5dexC ![]() 5vihC ![]() 5vijC ![]() 4nf8S 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: 33340.031 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 31785.299 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 426 molecules ![](data/chem/img/GLY.gif)
![](data/chem/img/5DY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/5DY.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/TRS.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-GLY / |
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#4: Chemical | ChemComp-5DY / |
#5: Chemical | ChemComp-PEG / |
#6: Chemical | ChemComp-TRS / |
#7: Water | ChemComp-HOH / |
-Details
Sequence details | THIS SAMPLE SEQUENCE MATCHES WITH NCBI REFERENCE SEQUENCE NP_036705.3 FOR GLUN2A |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonia Acetate, PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2015 |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 1.951→20.01 Å / Num. obs: 42271 / % possible obs: 97.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 21.6 Å2 / Rsym value: 0.108 / Net I/σ(I): 7.59 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 3721 / Rsym value: 0.476 / % possible all: 87 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4NF8 Resolution: 1.951→20.006 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.98 / 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: 1.951→20.006 Å
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Refine LS restraints |
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LS refinement shell |
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