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- PDB-5dt6: Crystal structure of the Drosophila GluR1A ligand binding domain ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5dt6 | ||||||
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Title | Crystal structure of the Drosophila GluR1A ligand binding domain complex with glutamate | ||||||
![]() | Glutamate receptor 1 | ||||||
![]() | MEMBRANE PROTEIN | ||||||
Function / homology | ![]() Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor activity / monoatomic cation transport / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential ...Activation of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Synaptic adhesion-like molecules / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor activity / monoatomic cation transport / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / postsynaptic density membrane / modulation of chemical synaptic transmission / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dharkar, P. / Mayer, M.L. | ||||||
![]() | ![]() Title: Novel Functional Properties of Drosophila CNS Glutamate Receptors. Authors: Li, Y. / Dharkar, P. / Han, T.H. / Serpe, M. / Lee, C.H. / Mayer, M.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.5 KB | Display | ![]() |
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PDB format | ![]() | 139.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5dtbC ![]() 5ehmC ![]() 5ehsC ![]() 5ictC ![]() 1s50S 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: 30566.738 Da / Num. of mol.: 1 / Fragment: unp residues 474-594; unp residues 739-880 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-GLU / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Sample buffer 150 NaCl, 10 Tris pH 8.5, 2 glutamate, 1 EDTA, 10% glycerol Reservoir 13% PEG 8K, 100 Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→50 Å / Num. obs: 46081 / % possible obs: 98.4 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.42 / % possible all: 95.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S50 Resolution: 1.598→29.176 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.95 / 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: 1.598→29.176 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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