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Yorodumi- PDB-3qu8: Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in... -
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-Basic information
Entry | Database: PDB / ID: 3qu8 | ||||||
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Title | Crystal structure of a human cytochrome P450 2B6 (Y226H/K262R) in complex with the inhibitor 4-(4-Nitrobenzyl)pyridine. | ||||||
Components | Cytochrome P450 2B6 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / P450 / CYTOCHROME P450 2B6 / MONOOXYGENASE / MEMBRANE PROTEIN / CYP2B6 / ENDOPLASMIC RETICULUM / HEME / IRON / MEMBRANE / METAL BINDING / MICROSOME / PHOSPHOPROTEIN / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity ...testosterone 16-alpha-hydroxylase activity / testosterone 16-beta-hydroxylase activity / Fatty acids / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / cellular ketone metabolic process / arachidonic acid epoxygenase activity / CYP2E1 reactions / epoxygenase P450 pathway / estrogen 2-hydroxylase activity / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / 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 / Phase I - Functionalization of compounds / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / monooxygenase activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / endoplasmic reticulum membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Shah, M.B. / Pascual, J. / Stout, C.D. / Halpert, J.R. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2011 Title: Structures of Cytochrome P450 2B6 Bound to 4-Benzylpyridine and 4-(4-Nitrobenzyl)pyridine: Insight into Inhibitor Binding and Rearrangement of Active Site Side Chains. Authors: Shah, M.B. / Pascual, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R. | ||||||
History |
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Remark 999 | THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) ...THE RESIDUES 3-21 (LSVLLFLALLTGLLLLLVQ) OF CORRESPONDING DATABASE REFERENCE SEQUENCE (UNP P20813) IS DELETED IN THIS STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qu8.cif.gz | 557.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qu8.ent.gz | 462.1 KB | Display | PDB format |
PDBx/mmJSON format | 3qu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/3qu8 ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3qu8 | HTTPS FTP |
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-Related structure data
Related structure data | 3qoaC 3ibdS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 54646.004 Da / Num. of mol.: 6 / Fragment: Cytochrome P450 2B6, residues 3-21 deleted Mutation: E2A, R22K, H23K, P24T, N25S, T26S, H27K, D28G, R29K, Y226H, K262R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Plasmid: pKK / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P20813, unspecific monooxygenase #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-3QU / #4: Chemical | ChemComp-CM5 / #5: 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: 2.74 Å3/Da / Density % sol: 55.06 % |
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Crystal grow | Temperature: 291 K / pH: 7 Details: 0.15 M DL-Malic Acid, 20 % w/v PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 11, 2010 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→84.6 Å / Num. obs: 76085 / % possible obs: 88.9 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 52.67 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.368 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3IBD Resolution: 2.8→50.51 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.884 / SU B: 16.814 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.67 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50.51 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.8→2.88 Å / Total num. of bins used: 20
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