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- PDB-2fdv: Microsomal P450 2A6 with the inhibitor N-Methyl(5-(pyridin-3-yl)f... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fdv | ||||||
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Title | Microsomal P450 2A6 with the inhibitor N-Methyl(5-(pyridin-3-yl)furan-2-yl)methanamine bound | ||||||
![]() | Cytochrome P450 2A6 | ||||||
![]() | OXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / MONOOXYGENASE / DRUG METABOLIZING ENZYME / COUMARIN 7-HYDROXYLASE / NICOTINE OXIDASE | ||||||
Function / homology | ![]() coumarin catabolic process / coumarin 7-hydroxylase activity / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / 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 / steroid metabolic process ...coumarin catabolic process / coumarin 7-hydroxylase activity / coumarin metabolic process / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / 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 / steroid metabolic process / cytoplasmic microtubule / xenobiotic catabolic process / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yano, J.K. / Stout, C.D. / Johnson, E.F. | ||||||
![]() | ![]() Title: Synthetic Inhibitors of Cytochrome P-450 2A6: Inhibitory Activity, Difference Spectra, Mechanism of Inhibition, and Protein Cocrystallization. Authors: Yano, J.K. / Denton, T.T. / Cerny, M.A. / Zhang, X. / Johnson, E.F. / Cashman, J.R. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES 1-28 WERE REPLACED WITH THE SEQUENCE MAKKTS |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 414.8 KB | Display | ![]() |
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PDB format | ![]() | 335.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 84.1 KB | Display | |
Data in CIF | ![]() | 121.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2fduC ![]() 2fdwC ![]() 2fdyC ![]() 1z10S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54671.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 1457 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/D2G.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/D2G.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-D2G / #5: Chemical | ChemComp-EDO / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Polyethylene Glycol2000, Monomethyl Ether, TRIS, AMMONIUM SULFATE, ANAPOE-X-405 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2005 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.8 Å / Num. all: 294239 / Num. obs: 278644 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.045 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.662 / % possible all: 70.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Z10 Resolution: 1.65→33.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→33.8 Å
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Refine LS restraints |
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