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Yorodumi- PDB-6e5v: human mGlu8 receptor amino terminal domain in complex with (S)-3,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6e5v | ||||||
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Title | human mGlu8 receptor amino terminal domain in complex with (S)-3,4-Dicarboxyphenylglycine (DCPG) | ||||||
Components | Metabotropic glutamate receptor 8 | ||||||
Keywords | SIGNALING PROTEIN / mGluR8 ATD / GRM8 / DCPG | ||||||
Function / homology | Function and homology information group III metabotropic glutamate receptor activity / adenylate cyclase-inhibiting G protein-coupled glutamate receptor signaling pathway / G protein-coupled glutamate receptor signaling pathway / Class C/3 (Metabotropic glutamate/pheromone receptors) / glutamate receptor activity / regulation of synaptic transmission, glutamatergic / visual perception / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / G protein-coupled receptor activity / G alpha (i) signalling events / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Chen, Q. / Ho, J.D. / Ashok, S. / Vargas, M.C. / Wang, J. / Atwell, S. / Bures, M. / Schkeryantz, J.M. / Monn, J.A. / Hao, J. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Structural Basis for ( S)-3,4-Dicarboxyphenylglycine (DCPG) As a Potent and Subtype Selective Agonist of the mGlu8Receptor. Authors: Chen, Q. / Ho, J.D. / Ashok, S. / Vargas, M.C. / Wang, J. / Atwell, S. / Bures, M. / Schkeryantz, J.M. / Monn, J.A. / Hao, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e5v.cif.gz | 182.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e5v.ent.gz | 141.5 KB | Display | PDB format |
PDBx/mmJSON format | 6e5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e5v_validation.pdf.gz | 474.1 KB | Display | wwPDB validaton report |
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Full document | 6e5v_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 6e5v_validation.xml.gz | 31.6 KB | Display | |
Data in CIF | 6e5v_validation.cif.gz | 42.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e5/6e5v ftp://data.pdbj.org/pub/pdb/validation_reports/e5/6e5v | HTTPS FTP |
-Related structure data
Related structure data | 6bszS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58832.715 Da / Num. of mol.: 2 / Mutation: C246S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GRM8, GPRC1H, MGLUR8 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O00222 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.21 Å3/Da / Density % sol: 44.44 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 100mM Bis-Tris, pH 6.5, 27% PEG 3350, 200mM Sodium Acetate |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 11, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→19.91 Å / Num. obs: 21256 / % possible obs: 99.3 % / Redundancy: 6.2 % / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.95→3.11 Å / Mean I/σ(I) obs: 1.5 / Rsym value: 0.91 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6BSZ Resolution: 2.95→19.82 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.89 / SU B: 26.279 / SU ML: 0.467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.52 Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 110.15 Å2 / Biso mean: 66.96 Å2 / Biso min: 28.42 Å2
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Refinement step | Cycle: final / Resolution: 2.95→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.952→3.027 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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