+Open data
-Basic information
Entry | Database: PDB / ID: 3e6i | ||||||
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Title | Human cytochrome P450 2E1 in complex with the inhibitor indazole | ||||||
Components | Cytochrome P450 2E1 | ||||||
Keywords | OXIDOREDUCTASE / CYP2E1 / P450 2E1 / monooxygenase / acetaminophen / heme / Endoplasmic reticulum / Iron / Membrane / Metal-binding / Microsome | ||||||
Function / homology | Function and homology information : / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Porubsky, P.R. / Meneely, K.M. / Scott, E.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structures of human cytochrome P450 2E1: insights into the binding of inhibitors and both small molecular weight and fatty acid substrates. Authors: Porubsky, P.R. / Meneely, K.M. / Scott, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3e6i.cif.gz | 200.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e6i.ent.gz | 159.2 KB | Display | PDB format |
PDBx/mmJSON format | 3e6i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3e6i_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3e6i_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3e6i_validation.xml.gz | 37.1 KB | Display | |
Data in CIF | 3e6i_validation.cif.gz | 50.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/3e6i ftp://data.pdbj.org/pub/pdb/validation_reports/e6/3e6i | HTTPS FTP |
-Related structure data
Related structure data | 3e4eC 2p85S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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: Residues 32-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2E1, CYP2E / Plasmid: pkk2E1dH / Production host: Escherichia coli (E. coli) / Strain (production host): TOPP3 / References: UniProt: P05181, unspecific monooxygenase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.58 Å3/Da / Density % sol: 52.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 11% v/v isopropanol, 6% PEG MME 2000, 0.1M Na HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 15, 2008 / Details: Mirrors |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal. Asymmetric cut 12.2 degs. Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→112.51 Å / Num. all: 56315 / Num. obs: 56268 / % possible obs: 99.7 % / Redundancy: 5.9 % / Biso Wilson estimate: 41.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4154 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2P85 Resolution: 2.2→41.78 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 7.582 / SU ML: 0.192 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.243 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 max: 77.27 Å2 / Biso mean: 39.91 Å2 / Biso min: 13.81 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→41.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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