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- PDB-6vlt: Crystal Structure of Human P450 2C9*2 Genetic Variant in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6vlt | ||||||
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Title | Crystal Structure of Human P450 2C9*2 Genetic Variant in Complex with Losartan | ||||||
![]() | Cytochrome P450 2C9 | ||||||
![]() | OXIDOREDUCTASE / CYP2C9*2 / CYP2C9 R144C | ||||||
Function / homology | ![]() 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 / xenobiotic metabolic process / cholesterol metabolic process / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shah, M.B. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Cytochrome P450 2C9*2 in Complex with Losartan: Insights into the Effect of Genetic Polymorphism. Authors: Parikh, S.J. / Evans, C.M. / Obi, J.O. / Zhang, Q. / Maekawa, K. / Glass, K.C. / Shah, M.B. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 733.4 KB | Display | ![]() |
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PDB format | ![]() | 606.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 6.7 MB | Display | ![]() |
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Full document | ![]() | 6.8 MB | Display | |
Data in XML | ![]() | 141.6 KB | Display | |
Data in CIF | ![]() | 182.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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7 | ![]()
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8 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 54181.762 Da / Num. of mol.: 8 / Mutation: R144C, V490I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P11712, unspecific monooxygenase, (R)-limonene 6-monooxygenase, (S)-limonene 6-monooxygenase, (S)-limonene 7-monooxygenase |
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-Non-polymers , 5 types, 170 molecules ![](data/chem/img/HEM.gif)
![](data/chem/img/LSN.gif)
![](data/chem/img/CM5.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/LSN.gif)
![](data/chem/img/CM5.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-LSN / [ #4: Chemical | ChemComp-CM5 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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Sequence details | THE N-TERMINAL TRANSMEMBR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.26 Å3/Da / Density % sol: 71.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1M Lithium sulfate monohydrate, 0.1M Sodium citrate tribasic dehydrate pH 5.5, 20% w/v Polyethylene glycol 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.12→50.01 Å / Num. obs: 122890 / % possible obs: 99.3 % / Redundancy: 8.1 % / Rpim(I) all: 0.127 / Rrim(I) all: 0.367 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 3.12→3.29 Å / Redundancy: 8.2 % / Mean I/σ(I) obs: 2.5 / Num. unique obs: 17998 / Rpim(I) all: 1.2 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OG Resolution: 3.12→50.01 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.179 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.361 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 201.6 Å2 / Biso mean: 79.914 Å2 / Biso min: 20 Å2
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Refinement step | Cycle: final / Resolution: 3.12→50.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.122→3.203 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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