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- PDB-4kfq: Crystal structure of the NMDA receptor GluN1 ligand binding domai... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4kfq | ||||||
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Title | Crystal structure of the NMDA receptor GluN1 ligand binding domain in complex with 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one | ||||||
![]() | Glutamate receptor ionotropic, NMDA 1 | ||||||
![]() | MEMBRANE PROTEIN / ligand binding domain / Ionotropic Glutamate Receptor | ||||||
Function / homology | ![]() pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane ...pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / voltage-gated monoatomic cation channel activity / regulation of monoatomic cation transmembrane transport / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / RAF/MAP kinase cascade / parallel fiber to Purkinje cell synapse / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / suckling behavior / startle response / response to amine / monoatomic cation transmembrane transport / monoatomic cation transport / regulation of neuronal synaptic plasticity / 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 / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / 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 / 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 / positive regulation of synaptic transmission, glutamatergic / adult locomotory behavior / learning / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / calcium channel activity / visual learning / regulation of synaptic plasticity / response to organic cyclic compound / terminal bouton / cerebral cortex development / memory / synaptic vesicle membrane / intracellular calcium ion homeostasis / response to calcium ion / neuron cellular homeostasis / calcium ion transport / rhythmic process / synaptic vesicle / presynaptic membrane / signaling receptor activity / amyloid-beta binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / response to ethanol / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / dendritic spine / postsynaptic density / learning or memory Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Steffensen, T.B. / Tabrizi, F.M. / Gajhede, M. / Kastrup, J.S. | ||||||
![]() | ![]() Title: Crystal structure and pharmacological characterization of a novel N-methyl-D-aspartate (NMDA) receptor antagonist at the GluN1 glycine binding site. Authors: Kvist, T. / Steffensen, T.B. / Greenwood, J.R. / Mehrzad Tabrizi, F. / Hansen, K.B. / Gajhede, M. / Pickering, D.S. / Traynelis, S.F. / Kastrup, J.S. / Brauner-Osborne, H. #1: ![]() Title: Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA RECEPTOR NR1 ligand-binding core Authors: Furukawa, H. / Gouaux, 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 | ![]() | 141.9 KB | Display | ![]() |
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PDB format | ![]() | 110.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 484.4 KB | Display | ![]() |
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Full document | ![]() | 493.4 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 40.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1pbqS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 33340.031 Da / Num. of mol.: 2 / Fragment: UNP residues 394-554, 663-800 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUN1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 153 AND 154 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (394-554, 663-800) Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.56 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG ...Details: 1-thioxo-1,2-dihydro-[1,2,4]triazolo[4,3-a]quinoxalin-4(5H)-one was added as solid compound and the solution was gently shaken overnight. 0.3 M ammonium sulfate, 0.1 M HEPES, and 30 % PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→39.69 Å / Num. all: 37896 / Num. obs: 37846 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.9 / Num. unique all: 5498 / Rsym value: 0.392 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1PBQ Resolution: 2.2→39.69 Å / SU ML: 0.62 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 21.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.896 Å2 / ksol: 0.376 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→39.69 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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