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Yorodumi- PDB-4ksd: Structures of P-glycoprotein reveal its conformational flexibilit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ksd | ||||||
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Title | Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN / transporter / ATP binding / membrane | ||||||
Function / homology | Function and homology information hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus ...hormone transport / cellular response to borneol / response to codeine / response to cyclosporin A / Atorvastatin ADME / cellular response to mycotoxin / daunorubicin transport / positive regulation of response to drug / response to quercetin / cellular response to external biotic stimulus / regulation of intestinal absorption / response to antineoplastic agent / Prednisone ADME / positive regulation of establishment of Sertoli cell barrier / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / regulation of response to osmotic stress / cellular response to L-glutamate / ABC-family proteins mediated transport / establishment of blood-brain barrier / response to thyroxine / phosphatidylcholine floppase activity / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / xenobiotic detoxification by transmembrane export across the plasma membrane / export across plasma membrane / response to vitamin D / ABC-type xenobiotic transporter / intercellular canaliculus / transepithelial transport / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / response to vitamin A / response to glucagon / intestinal absorption / phospholipid translocation / cellular response to antibiotic / maintenance of blood-brain barrier / cellular hyperosmotic salinity response / cellular response to alkaloid / xenobiotic transmembrane transporter activity / efflux transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / placenta development / regulation of chloride transport / stem cell proliferation / cellular response to estradiol stimulus / brush border membrane / circadian rhythm / G2/M transition of mitotic cell cycle / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / ubiquitin protein ligase binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Lama glama (llama) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1001 Å | ||||||
Authors | Ward, A. / Szewczyk, P. / Grimard, V. / Lee, C.-W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. ...Ward, A. / Szewczyk, P. / Grimard, V. / Lee, C.-W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P. / Urbatsch, I. / Govaerts, C. / Steyaert, J. / Chang, G. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain. Authors: Ward, A.B. / Szewczyk, P. / Grimard, V. / Lee, C.W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P.G. / Urbatsch, I.L. / Govaerts, ...Authors: Ward, A.B. / Szewczyk, P. / Grimard, V. / Lee, C.W. / Martinez, L. / Doshi, R. / Caya, A. / Villaluz, M. / Pardon, E. / Cregger, C. / Swartz, D.J. / Falson, P.G. / Urbatsch, I.L. / Govaerts, C. / Steyaert, J. / Chang, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ksd.cif.gz | 259.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ksd.ent.gz | 213.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ksd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ks/4ksd ftp://data.pdbj.org/pub/pdb/validation_reports/ks/4ksd | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 141877.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abcb1a, Abcb4, Mdr1a, Mdr3, Pgy-3, Pgy3 / Production host: Komagataella pastoris (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase |
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#2: Antibody | Mass: 13809.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Gene: r2 / Production host: Escherichia coli (E. coli) |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.47 Å3/Da / Density % sol: 72.5 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Hepes (pH 7-8) and 22-27% (w/v) PEG 600, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 4.1→61.071 Å / Num. all: 23806 / Num. obs: 22783 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.1001→61.071 Å / SU ML: 0.68 / σ(F): 2.05 / Phase error: 34.19 / 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: 4.1001→61.071 Å
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Refine LS restraints |
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LS refinement shell |
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