+Open data
-Basic information
Entry | Database: PDB / ID: 5kpi | ||||||
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Title | Mouse native PGP | ||||||
Components | Multidrug resistance protein 1A | ||||||
Keywords | HYDROLASE / Mouse pgp / multidrug resistance / drug transport / native | ||||||
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 / negative regulation of sensory perception of pain / response to antineoplastic agent / positive regulation of establishment of Sertoli cell barrier / Prednisone ADME / response to alcohol / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / ceramide translocation / establishment of blood-retinal barrier / protein localization to bicellular tight junction / cellular response to L-glutamate / ABC-family proteins mediated transport / response to thyroxine / establishment of blood-brain barrier / phosphatidylethanolamine flippase activity / xenobiotic transport across blood-brain barrier / phosphatidylcholine floppase activity / xenobiotic detoxification by transmembrane export across the plasma membrane / intercellular canaliculus / export across plasma membrane / ABC-type xenobiotic transporter / response to vitamin D / P-type phospholipid transporter / ABC-type xenobiotic transporter activity / response to vitamin A / response to glucagon / intestinal absorption / phospholipid translocation / cellular response to antibiotic / cellular hyperosmotic salinity response / maintenance of blood-brain barrier / cellular response to alkaloid / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / cellular response to dexamethasone stimulus / response to cadmium ion / cellular response to estradiol stimulus / lactation / placenta development / response to progesterone / female pregnancy / brush border membrane / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / apical plasma membrane / response to xenobiotic stimulus / ATP hydrolysis activity / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.01 Å | ||||||
Authors | Xia, D. / Esser, L. / Zhou, F. | ||||||
Citation | Journal: J. Biol. Chem. / Year: 2017 Title: Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity. Authors: Esser, L. / Zhou, F. / Pluchino, K.M. / Shiloach, J. / Ma, J. / Tang, W.K. / Gutierrez, C. / Zhang, A. / Shukla, S. / Madigan, J.P. / Zhou, T. / Kwong, P.D. / Ambudkar, S.V. / Gottesman, M.M. / Xia, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kpi.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5kpi.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5kpi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kpi_validation.pdf.gz | 443.7 KB | Display | wwPDB validaton report |
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Full document | 5kpi_full_validation.pdf.gz | 451.7 KB | Display | |
Data in XML | 5kpi_validation.xml.gz | 74.4 KB | Display | |
Data in CIF | 5kpi_validation.cif.gz | 101.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kpi ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kpi | HTTPS FTP |
-Related structure data
Related structure data | 5ko2C 5koyC 5kpdC 5kpjC 4m1mS C: citing same article (ref.) 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: 141635.609 Da / Num. of mol.: 2 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 GS115 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase |
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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: 4.14 Å3/Da / Density % sol: 70.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 50 mM Glycine9.0 100 mM NaCl, 22-24% PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 4→35.405 Å / Num. obs: 37665 / % possible obs: 95.3 % / Redundancy: 5 % / Biso Wilson estimate: 186.57 Å2 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.035 / Rrim(I) all: 0.08 / Χ2: 0.999 / Net I/av σ(I): 16.956 / Net I/σ(I): 7.6 / Num. measured all: 187287 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M1M Resolution: 4.01→20.138 Å / SU ML: 0.6 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 35.2 / 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: 4.01→20.138 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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