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Yorodumi- PDB-5xxi: Crystal structure of CYP2C9 in complex with multiple losartan mol... -
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-Basic information
Entry | Database: PDB / ID: 5xxi | ||||||
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Title | Crystal structure of CYP2C9 in complex with multiple losartan molecules | ||||||
Components | Cytochrome P450 2C9 | ||||||
Keywords | OXIDOREDUCTASE / CYP2C9 / P450 2C9 | ||||||
Function / homology | Function and homology information arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process ...arachidonic acid 14,15-epoxygenase activity / arachidonic acid 11,12-epoxygenase activity / amide metabolic process / (S)-limonene 6-monooxygenase / (S)-limonene 7-monooxygenase / (R)-limonene 6-monooxygenase / (S)-limonene 6-monooxygenase activity / (S)-limonene 7-monooxygenase activity / (R)-limonene 6-monooxygenase activity / monocarboxylic acid metabolic process / urea metabolic process / Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) / omega-hydroxylase P450 pathway / CYP2E1 reactions / arachidonic acid epoxygenase activity / icosanoid biosynthetic process / epoxygenase P450 pathway / caffeine oxidase activity / Biosynthesis of maresin-like SPMs / Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) / monoterpenoid metabolic process / oxidative demethylation / Xenobiotics / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / long-chain fatty acid biosynthetic process / estrogen metabolic process / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / steroid hydroxylase activity / xenobiotic catabolic process / monooxygenase activity / cholesterol metabolic process / xenobiotic metabolic process / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Maekawa, K. / Adachi, M. / Shah, M.B. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: Structural Basis of Single-Nucleotide Polymorphisms in Cytochrome P450 2C9 Authors: Maekawa, K. / Adachi, M. / Matsuzawa, Y. / Zhang, Q. / Kuroki, R. / Saito, Y. / Shah, M.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xxi.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xxi.ent.gz | 86 KB | Display | PDB format |
PDBx/mmJSON format | 5xxi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xxi_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5xxi_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5xxi_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5xxi_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/5xxi ftp://data.pdbj.org/pub/pdb/validation_reports/xx/5xxi | HTTPS FTP |
-Related structure data
Related structure data | 5x23C 5x24C 1r9oS 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: 52763.121 Da / Num. of mol.: 1 / Fragment: UNP residues 28-490 / Mutation: V490I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2C9, CYP2C10 / Production host: Escherichia coli (E. coli) References: UniProt: P11712, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen ...References: UniProt: P11712, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor, EC: 1.14.13.80, EC: 1.14.13.48, EC: 1.14.13.49, EC: 1.14.99.38 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-K / | #5: 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: 4.08 Å3/Da / Density % sol: 69.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG-8000 and 0.1M HEPES pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→43.63 Å / Num. obs: 36523 / % possible obs: 99.2 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 30 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5747 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R9O Resolution: 2.3→43.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.309 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.04 / ESU R Free: 0.044 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.2 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→43.63 Å
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Refine LS restraints |
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