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- PDB-5l1f: AMPA subtype ionotropic glutamate receptor GluA2 in complex with ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l1f | ||||||
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Title | AMPA subtype ionotropic glutamate receptor GluA2 in complex with noncompetitive inhibitor Perampanel | ||||||
![]() | Glutamate receptor 2 | ||||||
![]() | TRANSPORT PROTEIN/INHIBITOR / Transporter / MEMBRANE PROTEIN / TRANSPORT PROTEIN / TRANSPORT PROTEIN-INHIBITOR complex | ||||||
Function / homology | ![]() spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / postsynaptic membrane / perikaryon / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Sobolevsky, A.I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural Bases of Noncompetitive Inhibition of AMPA-Subtype Ionotropic Glutamate Receptors by Antiepileptic Drugs. Authors: Yelshanskaya, M.V. / Singh, A.K. / Sampson, J.M. / Narangoda, C. / Kurnikova, M. / Sobolevsky, A.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 605.9 KB | Display | ![]() |
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PDB format | ![]() | 497.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 110.6 KB | Display | |
Data in CIF | ![]() | 143.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l1bC ![]() 5l1eC ![]() 5l1gC ![]() 5l1hC ![]() 3kg2S 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
#1: Protein | Mass: 89805.734 Da / Num. of mol.: 4 Fragment: UNP residues 25-847, with deletions of 397-398, 402-405, 566-587 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-6ZP / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.16 Å3/Da / Density % sol: 70.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 11-14% (w/v) PEG 6,000, 0.1 M ammonium phosphate and 0.1 M TRIS (pH 7.9-8.0) PH range: 7.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 4→49.57 Å / Num. obs: 51631 / % possible obs: 99.5 % / Observed criterion σ(I): 1.11 / Redundancy: 6.45 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 8.15 |
Reflection shell | Resolution: 4→4.14 Å / Redundancy: 5.55 % / Rmerge(I) obs: 0.9 / CC1/2: 0.49 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KG2 Resolution: 4→49.57 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 30.52 / 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: 4→49.57 Å
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Refine LS restraints |
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LS refinement shell |
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