+Open data
-Basic information
Entry | Database: PDB / ID: 9gj1 | ||||||
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Title | NMDA bound to compound 339 | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / ion transport ligand gated ion channel | ||||||
Function / homology | Function and homology information 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 / Assembly and cell surface presentation of NMDA receptors / 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 / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / Neurexins and neuroligins / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / positive regulation of reactive oxygen species biosynthetic process / glycine binding / positive regulation of calcium ion transport into cytosol / monoatomic cation transmembrane transport / startle response / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / dopamine metabolic process / regulation of neuronal synaptic plasticity / monoatomic cation transport / Long-term potentiation / ligand-gated monoatomic ion channel activity / positive regulation of excitatory postsynaptic potential / excitatory synapse / synaptic cleft / calcium ion homeostasis / glutamate-gated calcium ion channel activity / sensory perception of pain / EPHB-mediated forward signaling / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / response to amphetamine / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / neurogenesis / excitatory postsynaptic potential / regulation of membrane potential / long-term synaptic potentiation / synaptic membrane / visual learning / protein catabolic process / brain development / postsynaptic density membrane / negative regulation of protein catabolic process / regulation of synaptic plasticity / terminal bouton / memory / calcium ion transmembrane transport / response to wounding / synaptic vesicle / signaling receptor activity / presynaptic membrane / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / response to ethanol / postsynaptic membrane / dendritic spine / calmodulin binding / postsynaptic density / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / dendrite / synapse / calcium ion binding / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å | ||||||
Authors | Carr, K.H. / Ascic, E. / Leonard, P.M. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Advancements in NMDA Receptor-Targeted Antidepressants: From d-Cycloserine Discovery to Preclinical Efficacy of Lu AF90103. Authors: Ascic, E. / Marigo, M. / David, L. / Frisch Herrik, K. / Grupe, M. / Hougaard, C. / Mork, A. / Jones, C.R. / Badolo, L. / Frederiksen, K. / Boonen, H.C.M. / Jensen, H.S. / Kilburn, J.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 9gj1.cif.gz | 234.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb9gj1.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 9gj1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 9gj1_validation.pdf.gz | 758.8 KB | Display | wwPDB validaton report |
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Full document | 9gj1_full_validation.pdf.gz | 762.6 KB | Display | |
Data in XML | 9gj1_validation.xml.gz | 29 KB | Display | |
Data in CIF | 9gj1_validation.cif.gz | 40.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gj/9gj1 ftp://data.pdbj.org/pub/pdb/validation_reports/gj/9gj1 | HTTPS FTP |
-Related structure data
Related structure data | 9gibC 9gicC 9gidC 9gieC 9gifC 9gigC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 31939.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin2a, HJG63_005955 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: G3V9C5, UniProt: A0A7J8EZV6 |
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#2: Protein | Mass: 33264.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami (DE3) / References: UniProt: Q05586 |
-Non-polymers , 4 types, 361 molecules
#3: Chemical | ChemComp-GLU / |
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#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-A1IME / ( Mass: 279.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H13N3O3S / Feature type: SUBJECT OF INVESTIGATION |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.82 % |
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Crystal grow | Temperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10-15% PEG 3350, 0.1 M HEPES pH 7.0, 1 mM sodium azide, 1% tryptone |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.62→59.85 Å / Num. obs: 71100 / % possible obs: 96.9 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.62→1.66 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4136 / CC1/2: 0.487 / Rpim(I) all: 0.582 / % possible all: 78.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→59.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.553 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.646 Å2
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Refinement step | Cycle: LAST / Resolution: 1.62→59.85 Å
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Refine LS restraints |
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LS refinement shell |
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