+Open data
-Basic information
Entry | Database: PDB / ID: 6ujn | ||||||
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Title | P-glycoprotein mutant-C952A-with BDE100 | ||||||
Components | ATP-dependent translocase ABCB1 | ||||||
Keywords | TRANSLOCASE / P-glycoprotein / MDR1 / P-gp / Pgp / Multidrug Resistance 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 / ABC-type xenobiotic transporter / response to vitamin D / 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: 3.98 Å | ||||||
Authors | Aller, S.G. / Le, C.A. | ||||||
Citation | Journal: Iucrj / Year: 2020 Title: Structural definition of polyspecific compensatory ligand recognition by P-glycoprotein. Authors: Le, C.A. / Harvey, D.S. / Aller, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ujn.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ujn.ent.gz | 190.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ujn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ujn_validation.pdf.gz | 675.1 KB | Display | wwPDB validaton report |
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Full document | 6ujn_full_validation.pdf.gz | 695.5 KB | Display | |
Data in XML | 6ujn_validation.xml.gz | 42.3 KB | Display | |
Data in CIF | 6ujn_validation.cif.gz | 57 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uj/6ujn ftp://data.pdbj.org/pub/pdb/validation_reports/uj/6ujn | HTTPS FTP |
-Related structure data
Related structure data | 6ujpC 6ujrC 6ujsC 6ujtC 6ujwC 4xwkS S: Starting model for refinement C: citing same article (ref.) |
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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: 141645.625 Da / Num. of mol.: 1 / Mutation: N83Q,N87Q, N90Q,C952A 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, ABC-type xenobiotic transporter, P-type phospholipid transporter |
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#2: Chemical | ChemComp-4C8 / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.99 Å3/Da / Density % sol: 69.16 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: Hepes, lithium sulfate, EDTA, and 26-28.5% (w/v) polyethylene glycol (PEG) 600 (pH 7.9 to 8.4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91959 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.91959 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.98→50 Å / Num. obs: 36876 / % possible obs: 100 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.022 / Rrim(I) all: 0.078 / Χ2: 0.523 / Net I/σ(I): 3.8 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4xwk without BDE100 Resolution: 3.98→29.95 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.19 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 312.21 Å2 / Biso mean: 190.8707 Å2 / Biso min: 113.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.98→29.95 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22
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