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- PDB-3gph: Human cytochrome P450 2E1 in complex with omega-imidazolyl-decano... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gph | ||||||
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Title | Human cytochrome P450 2E1 in complex with omega-imidazolyl-decanoic acid | ||||||
![]() | Cytochrome P450 2E1 | ||||||
![]() | OXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / fatty acid hydroxylase / Metal-binding | ||||||
Function / homology | ![]() : / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity ...: / 4-nitrophenol 2-monooxygenase activity / carbon tetrachloride metabolic process / benzene metabolic process / 4-nitrophenol metabolic process / halogenated hydrocarbon metabolic process / long-chain fatty acid omega-1 hydroxylase activity / long-chain fatty acid metabolic process / CYP2E1 reactions / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / lipid hydroxylation / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / : / Xenobiotics / Paracetamol ADME / 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 / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid metabolic process / Hsp70 protein binding / monooxygenase activity / xenobiotic metabolic process / response to bacterium / Hsp90 protein binding / oxygen binding / mitochondrial inner membrane / oxidoreductase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / enzyme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Porubsky, P.R. / Battaile, K.P. / Scott, E.E. | ||||||
![]() | ![]() Title: Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode. Authors: Porubsky, P.R. / Battaile, K.P. / 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 | ![]() | 197.8 KB | Display | ![]() |
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PDB format | ![]() | 157 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.7 KB | Display | |
Data in CIF | ![]() | 48.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3kohC ![]() 3lc4C ![]() 3e61S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 55058.488 Da / Num. of mol.: 2 / Fragment: UNP residues 32-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na HEPES, 5% Isopropanol, 20% PEG 2000 MME, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 2, 2008 Details: Sagitally focused second crystal, vertical focusing via a one-meter, Pt/Pd-coated cylindrically focusing mirror |
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. all: 28495 / Num. obs: 28493 / % possible obs: 95.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 51.075 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 17.071 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.457 / Num. unique all: 2034 / % possible all: 93.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 3E61 Resolution: 2.7→31.31 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.86 / SU B: 14.75 / SU ML: 0.301 / Cross valid method: THROUGHOUT / ESU R Free: 0.42 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.748 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→31.31 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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