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Yorodumi- PDB-5x24: Crystal structure of CYP2C9 genetic variant I359L (*3) in complex... -
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-Basic information
Entry | Database: PDB / ID: 5x24 | |||||||||
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Title | Crystal structure of CYP2C9 genetic variant I359L (*3) in complex with multiple losartan molecules | |||||||||
Components | Cytochrome P450 2C9 | |||||||||
Keywords | OXIDOREDUCTASE / CYP2C9 polymorphic mutant / Single Nucleotide Polymorphism / P450 2C9 genetic variant | |||||||||
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: 2.48 Å | |||||||||
Authors | Maekawa, K. / Adachi, M. / Shah, M.B. | |||||||||
Funding support | Japan, 2items
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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 | 5x24.cif.gz | 112.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5x24.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 5x24.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5x24_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 5x24_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5x24_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 5x24_validation.cif.gz | 30.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x2/5x24 ftp://data.pdbj.org/pub/pdb/validation_reports/x2/5x24 | HTTPS FTP |
-Related structure data
Related structure data | 5x23C 5xxiC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 54235.812 Da / Num. of mol.: 1 / Fragment: UNP residues 24-490 / Mutation: I359L, V490I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2C9, CYP2C10 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 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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-Non-polymers , 5 types, 61 molecules
#2: Chemical | ChemComp-HEM / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-K / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | The N-terminal transmembrane anchor domain (residues 1-23 in P11712) was replaced with MAKKT. |
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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: 4.04 Å3/Da / Density % sol: 69.55 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 1.8M ammonium sulfate, 0.1M BIS-TRIS pH 6.5 and 2% (v/v) Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 3, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.48→35.78 Å / Num. obs: 30693 / % possible obs: 98.38 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 55.2 |
Reflection shell | Resolution: 2.481→2.545 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 1907 / % possible all: 88.21 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R9O Resolution: 2.48→35.78 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.706 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.253 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.852 Å2
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Refinement step | Cycle: 1 / Resolution: 2.48→35.78 Å
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Refine LS restraints |
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