+Open data
-Basic information
Entry | Database: PDB / ID: 3lsw | ||||||
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Title | Aniracetam bound to the ligand binding domain of GluA3 | ||||||
Components | GluA2 S1S2 domain | ||||||
Keywords | TRANSPORT PROTEIN / glutamate receptor / GluR3 / GluA3 / AMPA receptor / neurotransmitter receptor / S1S2 / allosteric modulator | ||||||
Function / homology | Function and homology information Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / chemical synaptic transmission, postsynaptic / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors ...Activation of AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / Trafficking of AMPA receptors / chemical synaptic transmission, postsynaptic / Trafficking of GluR2-containing AMPA receptors / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane potential / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / monoatomic ion transmembrane transport / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendritic shaft / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / terminal bouton / presynaptic membrane / amyloid-beta binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuronal cell body / glutamatergic synapse / dendrite / protein-containing complex / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 Å | ||||||
Authors | Ahmed, A.H. / Oswald, R.E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Piracetam Defines a New Binding Site for Allosteric Modulators of alpha-Amino-3-hydroxy-5-methyl-4-isoxazole-propionic Acid (AMPA) Receptors. Authors: Ahmed, A.H. / Oswald, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3lsw.cif.gz | 74.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3lsw.ent.gz | 53.2 KB | Display | PDB format |
PDBx/mmJSON format | 3lsw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/3lsw ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3lsw | HTTPS FTP |
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-Related structure data
Related structure data | 3lsfC 3lslC 3lsxC 3dp6S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28956.418 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Mus musculus (house mouse) Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P19492, UniProt: Q9Z2W9 | ||
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#2: Chemical | ChemComp-GLU / | ||
#3: Chemical | ChemComp-4MP / | ||
#4: Chemical | #5: 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: 2.63 Å3/Da / Density % sol: 53.25 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 16-18% PEG8K, 0.1 M Na Cacodylate, 0.1-0.15 M zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.977 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 8, 2009 |
Radiation | Monochromator: RH COATED SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. obs: 30548 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 43.056 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.19 / Num. unique all: 1410 / Rsym value: 0.298 / % possible all: 93.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3DP6 Resolution: 1.752→23.732 Å / SU ML: 0.21 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.17 / 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 / Bsol: 59.32 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 2.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.752→23.732 Å
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Refine LS restraints |
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LS refinement shell |
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