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Yorodumi- PDB-5uda: Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monot... -
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-Basic information
Entry | Database: PDB / ID: 5uda | ||||||
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Title | Crystal structure of CYP2B6 (Y226H/K262R) in complex with a monoterpene bornane | ||||||
Components | Cytochrome P450 2B6 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / CYP2B6 | ||||||
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 / CYP2E1 reactions / arachidonic acid epoxygenase activity / 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 / CYP2E1 reactions / arachidonic acid epoxygenase activity / 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 / monooxygenase activity / xenobiotic metabolic process / 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: 1.93 Å | ||||||
Authors | Shah, M.B. / Halpert, J.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Halogen-pi Interactions in the Cytochrome P450 Active Site: Structural Insights into Human CYP2B6 Substrate Selectivity. Authors: Shah, M.B. / Liu, J. / Zhang, Q. / Stout, C.D. / Halpert, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uda.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uda.ent.gz | 167.5 KB | Display | PDB format |
PDBx/mmJSON format | 5uda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5uda_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 5uda_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5uda_validation.xml.gz | 42.2 KB | Display | |
Data in CIF | 5uda_validation.cif.gz | 59.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/5uda ftp://data.pdbj.org/pub/pdb/validation_reports/ud/5uda | HTTPS FTP |
-Related structure data
Related structure data | 5uapC 5uecC 5ufgC 4i91S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 54646.004 Da / Num. of mol.: 2 / Mutation: Y226H, K262R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2B6 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 References: UniProt: P20813, 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 #2: Chemical | #3: Chemical | #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: 3.24 Å3/Da / Density % sol: 62.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 0.2 M Sodium Chloride 0.1 M HEPES 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: Marm / Detector: CCD / Date: Apr 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40.43 Å / Num. obs: 98894 / % possible obs: 96.2 % / Redundancy: 3.1 % / Rsym value: 0.049 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 3.2 / Num. unique all: 14692 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I91 Resolution: 1.93→40.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.804 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.123 / 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: 26.458 Å2
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Refinement step | Cycle: 1 / Resolution: 1.93→40.43 Å
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