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- PDB-4eji: Human Cytochrome P450 2A13 in complex with two molecules of 4-(me... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4eji | ||||||
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Title | Human Cytochrome P450 2A13 in complex with two molecules of 4-(methylnitrosamino)-1-(3-puridyl)-1-butanone | ||||||
![]() | Cytochrome P450 2A13 | ||||||
![]() | OXIDOREDUCTASE / CYP2A13 / cytochrome P450 2A13 / P450 2A13 / heme protein / monooxygenase / drug metabolism / xenobiotic metabolism / endoplasmic reticulum / membrane | ||||||
Function / homology | ![]() coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / 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 ...coumarin 7-hydroxylase activity / Fatty acids / coumarin metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / aflatoxin metabolic process / Aflatoxin activation and detoxification / 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 / unspecific monooxygenase / aromatase activity / monooxygenase activity / xenobiotic metabolic process / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | DeVore, N.M. / Scott, E.E. | ||||||
![]() | ![]() Title: Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes. Authors: DeVore, N.M. / Scott, E.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.9 KB | Display | ![]() |
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PDB format | ![]() | 84.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 824.6 KB | Display | ![]() |
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Full document | ![]() | 836.2 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ejgC ![]() 4ejhC ![]() 4ejjC ![]() 2p85S 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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Unit cell |
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Components
#1: Protein | Mass: 54804.758 Da / Num. of mol.: 1 / Fragment: unp residues 31-494 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-HEM / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.18 % |
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Crystal grow | Temperature: 298 K / pH: 7.8 Details: 4.0 M sodium formate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 27, 2012 / Details: RH COAT FLAT MIRROR, TOROIDAL FOCUSING MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→97.11 Å / Num. obs: 43580 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.104 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 14.8 % / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2P85 Resolution: 2.1→51.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.629 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.155 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.98 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→51.9 Å
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LS refinement shell | Resolution: 2.1→2.154 Å / Total num. of bins used: 20
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