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Yorodumi- PDB-3s2v: Crystal Structure of the Ligand Binding Domain of GluK1 in Comple... -
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-Basic information
Entry | Database: PDB / ID: 3s2v | ||||||
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Title | Crystal Structure of the Ligand Binding Domain of GluK1 in Complex with an Antagonist (S)-1-(2'-Amino-2'-carboxyethyl)-3-[(2-carboxythien-3-yl)methyl]thieno[3,4-d]pyrimidin-2,4-dione at 2.5 A Resolution | ||||||
Components | Glutamate receptor, ionotropic kainate 1 | ||||||
Keywords | MEMBRANE PROTEIN / antagonist / Ionotropic Glutamate Receptor | ||||||
Function / homology | Function and homology information gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential ...gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / synaptic transmission, GABAergic / glutamate binding / adult behavior / behavioral response to pain / modulation of excitatory postsynaptic potential / membrane depolarization / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / glutamate-gated receptor activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / ionotropic glutamate receptor signaling pathway / excitatory postsynaptic potential / SNARE binding / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / establishment of localization in cell / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / postsynaptic density membrane / modulation of chemical synaptic transmission / regulation of synaptic plasticity / terminal bouton / presynaptic membrane / nervous system development / scaffold protein binding / chemical synaptic transmission / postsynaptic density / receptor complex / neuronal cell body / glutamatergic synapse / synapse / dendrite / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Venskutonyte, R. / Frydenvang, K. / Kastrup, J.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Selective kainate receptor (GluK1) ligands structurally based upon 1H-cyclopentapyrimidin-2,4(1H,3H)-dione: synthesis, molecular modeling, and pharmacological and biostructural characterization. Authors: Venskutonyte, R. / Butini, S. / Coccone, S.S. / Gemma, S. / Brindisi, M. / Kumar, V. / Guarino, E. / Maramai, S. / Valenti, S. / Amir, A. / Valades, E.A. / Frydenvang, K. / Kastrup, J.S. / ...Authors: Venskutonyte, R. / Butini, S. / Coccone, S.S. / Gemma, S. / Brindisi, M. / Kumar, V. / Guarino, E. / Maramai, S. / Valenti, S. / Amir, A. / Valades, E.A. / Frydenvang, K. / Kastrup, J.S. / Novellino, E. / Campiani, G. / Pickering, D.S. #1: Journal: Febs Lett. / Year: 2005 Title: Crystal structure of the kainate receptor GluR5 ligand-binding core in complex with (S)-glutamate. Authors: Naur, P. / Vestergaard, B. / Skov, L.K. / Egebjerg, J. / Gajhede, M. / Kastrup, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s2v.cif.gz | 122.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s2v.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 3s2v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s2v_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3s2v_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3s2v_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | 3s2v_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/3s2v ftp://data.pdbj.org/pub/pdb/validation_reports/s2/3s2v | HTTPS FTP |
-Related structure data
Related structure data | 2f34S 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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29108.453 Da / Num. of mol.: 2 / Fragment: unp residues 430-544 AND 667-805 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: GRIK1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P22756 |
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-Non-polymers , 5 types, 338 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE STRUCTURE IS REPRESENTATIVE OF SEGMENTS S1 AND S2 COMPRISING THE LIGAND BINDING DOMAIN OF THE ...THE STRUCTURE IS REPRESENTA |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.42 % |
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Crystal grow | Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 24.4% PEG4000, 0.3 M lithium sulfate, 0.1 M phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.3 Å / Num. obs: 21923 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 1.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 2F34 Resolution: 2.5→19.779 Å / SU ML: 0.75 / Isotropic thermal model: Restrained / σ(F): 1.34 / Phase error: 24.14 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.306 Å2 / ksol: 0.349 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.5→19.779 Å
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Refine LS restraints |
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LS refinement shell |
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