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Yorodumi- PDB-3ebs: Human Cytochrome P450 2A6 I208S/I300F/G301A/S369G in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ebs | ||||||
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Title | Human Cytochrome P450 2A6 I208S/I300F/G301A/S369G in complex with Phenacetin | ||||||
Components | Cytochrome P450 2A6 | ||||||
Keywords | OXIDOREDUCTASE / CYP2A6 / P450 2A6 / CYP2A13 / P450 2A13 / monooxygenase / oxidoreducatase / heme / endoplasmic reticulum / iron / membrane / metal-binding / microsome / phenacetin / Polymorphism | ||||||
Function / homology | Function and homology information 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 / arachidonic acid epoxygenase activity / CYP2E1 reactions / 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 / cytoplasmic microtubule ...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 / arachidonic acid epoxygenase activity / CYP2E1 reactions / 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 / cytoplasmic microtubule / steroid metabolic process / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | DeVore, N.M. / Scott, E.E. | ||||||
Citation | Journal: Drug Metab.Dispos. / Year: 2008 Title: Key residues controlling phenacetin metabolism by human cytochrome P4502A enzymes. Authors: DeVore, N.M. / Smith, B.D. / Urban, M.J. / 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 | 3ebs.cif.gz | 379.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ebs.ent.gz | 309.7 KB | Display | PDB format |
PDBx/mmJSON format | 3ebs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eb/3ebs ftp://data.pdbj.org/pub/pdb/validation_reports/eb/3ebs | HTTPS FTP |
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-Related structure data
Related structure data | 1z10S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 54663.574 Da / Num. of mol.: 4 / Fragment: UNP residues 29 to 494 / Mutation: I208S/I300F/G301A/S369G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A6, CYP2A3 / Plasmid: pkka2A6dH / Production host: Escherichia coli (E. coli) / Strain (production host): Topp3 / References: UniProt: P11509, unspecific monooxygenase #2: Chemical | ChemComp-HEM / #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: 2.68 Å3/Da / Density % sol: 54.09 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 3350, 0.10 M Tris, 0.2 M Ammonium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 28, 2008 |
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: 2.15→87.04 Å / Num. all: 270986 / Num. obs: 121786 / % possible obs: 97.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 10 / Redundancy: 2.2 % / Rmerge(I) obs: 0.059 |
Reflection shell | Resolution: 2.15→2.21 Å / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 1.6 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: CYP2A6 PDB Entry 1Z10 Resolution: 2.15→87.04 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.917 / SU B: 6.745 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.218 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: 39.389 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→87.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Total num. of bins used: 20
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