+Open data
-Basic information
Entry | Database: PDB / ID: 5kpj | ||||||
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Title | Mouse pgp methylated protein | ||||||
Components | Multidrug resistance protein 1A | ||||||
Keywords | HYDROLASE / Mouse pgp / multidrug resistance / drug transport / methylated protein | ||||||
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 / ceramide translocation / terpenoid transport / ceramide floppase activity / response to glycoside / floppase activity / establishment of blood-retinal barrier / protein localization to bicellular tight junction / ABC-type oligopeptide transporter activity / ABC-family proteins mediated transport / cellular response to L-glutamate / 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 / response to vitamin D / ABC-type xenobiotic transporter / P-type phospholipid transporter / response to vitamin A / ABC-type xenobiotic transporter activity / 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 / response to cadmium ion / lactation / cellular response to dexamethasone stimulus / cellular response to estradiol stimulus / response to progesterone / female pregnancy / brush border membrane / placenta development / circadian rhythm / cellular response to tumor necrosis factor / cellular response to lipopolysaccharide / response to hypoxia / response to xenobiotic stimulus / apical plasma membrane / 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: 3.5 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 | 5kpj.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kpj.ent.gz | 190.3 KB | Display | PDB format |
PDBx/mmJSON format | 5kpj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kpj_validation.pdf.gz | 433.1 KB | Display | wwPDB validaton report |
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Full document | 5kpj_full_validation.pdf.gz | 443.5 KB | Display | |
Data in XML | 5kpj_validation.xml.gz | 40.1 KB | Display | |
Data in CIF | 5kpj_validation.cif.gz | 53.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kpj ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kpj | HTTPS FTP |
-Related structure data
Related structure data | 5ko2C 5koyC 5kpdC 5kpiC 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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Unit cell |
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-Components
#1: Protein | Mass: 141719.797 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 GS115 (fungus) / References: UniProt: P21447, xenobiotic-transporting ATPase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: The protein was methylated in the presende of AMPPNP with formaldehyd and dimethyl amino borane and subsquently purifed by size exclusion chromatography. Crysallization with 50 mM Tris 7.5, ...Details: The protein was methylated in the presende of AMPPNP with formaldehyd and dimethyl amino borane and subsquently purifed by size exclusion chromatography. Crysallization with 50 mM Tris 7.5, 100 mM NaCl and 30% PEG550 MME |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.89 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.89 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.5→50 Å / Num. obs: 28399 / % possible obs: 94.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 109.56 Å2 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.048 / Rrim(I) all: 0.144 / Χ2: 1.005 / Net I/av σ(I): 8.686 / Net I/σ(I): 7.9 / Num. measured all: 177435 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4M1M Resolution: 3.5→21.451 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 40.39 / 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: 3.5→21.451 Å
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Refine LS restraints |
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LS refinement shell |
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