+Open data
-Basic information
Entry | Database: PDB / ID: 4jwx | ||||||
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Title | GluN2A ligand-binding core in complex with propyl-NHP5G | ||||||
Components | GluN2A | ||||||
Keywords | UNKNOWN FUNCTION / bilobed structure | ||||||
Function / homology | Function and homology information neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process / conditioned place preference ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / directional locomotion / response to environmental enrichment / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / serotonin metabolic process / conditioned place preference / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / 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 / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / regulation of NMDA receptor activity / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / glutamate binding / cellular response to zinc ion / action potential / spinal cord development / dopamine metabolic process / startle response / response to amine / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / modulation of excitatory postsynaptic potential / response to lithium ion / positive regulation of excitatory postsynaptic potential / cellular response to glycine / response to light stimulus / positive regulation of protein targeting to membrane / neuron development / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / cellular response to manganese ion / glutamate receptor binding / multicellular organismal response to stress / monoatomic cation channel activity / glutamate-gated receptor activity / 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 / positive regulation of synaptic transmission, glutamatergic / neurogenesis / protein tyrosine kinase binding / response to cocaine / learning / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / hippocampus development / long-term synaptic potentiation / cellular response to amino acid stimulus / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / response to nicotine / protein catabolic process / calcium channel activity / visual learning / modulation of chemical synaptic transmission / regulation of synaptic plasticity / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / response to organic cyclic compound / terminal bouton / cerebral cortex development / memory / cellular response to growth factor stimulus / response to wounding / response to calcium ion / calcium ion transport / calcium-dependent protein binding / rhythmic process / synaptic vesicle / presynaptic membrane / ATPase binding / scaffold protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Hansen, K.B. / Tajima, N. / Risgaard, R. / Perszyk, R.E. / Jorgensen, L. / Vance, K.M. / Ogden, K.K. / Clausen, R.P. / Furukawa, H. / Traynelis, S.F. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2013 Title: Structural determinants of agonist efficacy at the glutamate binding site of N-methyl-d-aspartate receptors. Authors: Hansen, K.B. / Tajima, N. / Risgaard, R. / Perszyk, R.E. / Jorgensen, L. / Vance, K.M. / Ogden, K.K. / Clausen, R.P. / Furukawa, H. / Traynelis, S.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jwx.cif.gz | 84.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jwx.ent.gz | 62.5 KB | Display | PDB format |
PDBx/mmJSON format | 4jwx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jwx_validation.pdf.gz | 435.9 KB | Display | wwPDB validaton report |
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Full document | 4jwx_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 4jwx_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 4jwx_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/4jwx ftp://data.pdbj.org/pub/pdb/validation_reports/jw/4jwx | HTTPS FTP |
-Related structure data
Related structure data | 4jwyC 1ftjS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31425.018 Da / Num. of mol.: 1 / Fragment: ligand binding domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: Q00959*PLUS |
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#2: Chemical | ChemComp-1N4 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 100 mM HEPES-NaOH, 10-18% PEG8000, 100 mM calcium acatate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 45212 / Num. obs: 44489 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.6 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1FTJ Resolution: 1.5→19.184 Å / SU ML: 0.1 / σ(F): 1.34 / σ(I): 2 / Phase error: 17.4 / 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: 1.5→19.184 Å
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Refine LS restraints |
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LS refinement shell |
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