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- PDB-4ntj: Structure of the human P2Y12 receptor in complex with an antithro... -
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Basic information
Entry | Database: PDB / ID: 4ntj | ||||||
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Title | Structure of the human P2Y12 receptor in complex with an antithrombotic drug | ||||||
![]() | P2Y purinoceptor 12,Soluble cytochrome b562,P2Y purinoceptor 12 | ||||||
![]() | MEMBRANE PROTEIN / human P2Y12 receptor / GPCR network / lipidic cubic phase / antithrombotic drug / GPCR / PSI-Biology / Structural Genomics / Signaling Protein / membrane | ||||||
Function / homology | ![]() visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration ...visual system development / positive regulation of integrin activation by cell surface receptor linked signal transduction / G protein-coupled ADP receptor activity / regulation of microglial cell migration / cerebral cortex radial glia-guided migration / P2Y receptors / cell body membrane / G protein-coupled purinergic nucleotide receptor activity / positive regulation of monoatomic ion transport / positive regulation of microglial cell migration / G protein-coupled adenosine receptor activity / hemostasis / cell projection membrane / regulation of chemotaxis / positive regulation of chemotaxis / substrate-dependent cell migration, cell extension / cell projection organization / positive regulation of ruffle assembly / positive regulation of cell adhesion mediated by integrin / lamellipodium assembly / cellular response to ATP / response to axon injury / monoatomic ion transport / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / guanyl-nucleotide exchange factor activity / establishment of localization in cell / calcium-mediated signaling / electron transport chain / platelet activation / ADP signalling through P2Y purinoceptor 12 / platelet aggregation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / periplasmic space / electron transfer activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / cell surface / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. ...Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q. / GPCR Network (GPCR) | ||||||
![]() | ![]() Title: Structure of the human P2Y12 receptor in complex with an antithrombotic drug Authors: Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / ...Authors: Zhang, K. / Zhang, J. / Gao, Z.-G. / Zhang, D. / Zhu, L. / Han, G.W. / Moss, S.M. / Paoletta, S. / Kiselev, E. / Lu, W. / Fenalti, G. / Zhang, W. / Muller, C.E. / Yang, H. / Jiang, H. / Cherezov, V. / Katritch, V. / Jacobson, K.A. / Stevens, R.C. / Wu, B. / Zhao, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 170.8 KB | Display | ![]() |
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PDB format | ![]() | 133.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1m6tS ![]() 3vw7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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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: 53248.879 Da / Num. of mol.: 1 / Mutation: D294N, M1007W, H1102I, R1106L Source method: isolated from a genetically manipulated source Details: Chimera protein of N-terminal residues 2-223 from P2Y12R (P2Y12_HUMAN), Soluble cytochrome b562 (C562_ECOLX), and C-terminal residues 224-342 from P2Y12R (P2Y12_HUMAN). Source: (gene. exp.) ![]() ![]() ![]() Gene: P2RY12, HORK3, cybC / Plasmid: pFASTBAC1 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-AZJ / | ||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.91 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.05-0.15M ammonium formate, 0.1M sodium cacodylate, pH 6.0-6.5, 25-35% PEG 400, 200M AZD1283, Lipidic Cubic Phase, temperature 293K PH range: 6.0-6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2013 / Details: mirror |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 19116 / % possible obs: 94.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 84.46 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 1.2 / Num. unique all: 1608 / % possible all: 79.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3VW7 (PAR1), PDB ENTRY 1M6T (BRIL) Resolution: 2.62→26.44 Å / Cor.coef. Fo:Fc: 0.9456 / Cor.coef. Fo:Fc free: 0.9344 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 Details: THERE ARE SOME UNKNOWN DENSITIES. LOCATED NEAR THE SIDE CHAIN OF TYR 32. THEY HAVE NOT BEEN MODELLED.
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Displacement parameters | Biso max: 225.79 Å2 / Biso mean: 106.1 Å2 / Biso min: 64.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.549 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.62→26.44 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.62→2.76 Å / Total num. of bins used: 10
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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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