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- PDB-5uec: Crystal Structure of CYP2B6 (Y226H/K262R) in complex with myrteny... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5uec | ||||||
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Title | Crystal Structure of CYP2B6 (Y226H/K262R) in complex with myrtenyl bromide. | ||||||
![]() | Cytochrome P450 2B6 | ||||||
![]() | OXIDOREDUCTASE / cytochrome P450 2B6 | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shah, M.B. / Halpert, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.2 KB | Display | ![]() |
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PDB format | ![]() | 86 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 21.3 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5uapC ![]() 5udaC ![]() 5ufgC ![]() 4i91S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 54646.004 Da / Num. of mol.: 1 / Mutation: Y226H, K262R Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() 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 | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | #4: Chemical | ChemComp-85D / ( | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2 M Magnesium acetate tetrahydrate 25%w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2015 / Details: Si(111) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99 Å / Relative weight: 1 |
Reflection | Resolution: 2.27→67.59 Å / Num. obs: 33225 / % possible obs: 100 % / Redundancy: 19.3 % / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.27→2.31 Å / Redundancy: 15 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1588 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4I91 Resolution: 2.27→47.55 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.039 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.212 / ESU R Free: 0.192 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.561 Å2
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Refinement step | Cycle: 1 / Resolution: 2.27→47.55 Å
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Refine LS restraints |
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