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Yorodumi- PDB-2fdv: Microsomal P450 2A6 with the inhibitor N-Methyl(5-(pyridin-3-yl)f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2fdv | ||||||
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Title | Microsomal P450 2A6 with the inhibitor N-Methyl(5-(pyridin-3-yl)furan-2-yl)methanamine bound | ||||||
Components | Cytochrome P450 2A6 | ||||||
Keywords | OXIDOREDUCTASE / CYP2A6 / P450 2A6 / P450 / MONOOXYGENASE / DRUG METABOLIZING ENZYME / COUMARIN 7-HYDROXYLASE / NICOTINE OXIDASE | ||||||
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 / CYP2E1 reactions / arachidonate epoxygenase activity / 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 / CYP2E1 reactions / arachidonate epoxygenase activity / 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 / endoplasmic reticulum membrane / heme binding / enzyme binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Yano, J.K. / Stout, C.D. / Johnson, E.F. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Synthetic Inhibitors of Cytochrome P-450 2A6: Inhibitory Activity, Difference Spectra, Mechanism of Inhibition, and Protein Cocrystallization. Authors: Yano, J.K. / Denton, T.T. / Cerny, M.A. / Zhang, X. / Johnson, E.F. / Cashman, J.R. | ||||||
History |
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Remark 999 | SEQUENCE RESIDUES 1-28 WERE REPLACED WITH THE SEQUENCE MAKKTS |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fdv.cif.gz | 414.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fdv.ent.gz | 335.9 KB | Display | PDB format |
PDBx/mmJSON format | 2fdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/2fdv ftp://data.pdbj.org/pub/pdb/validation_reports/fd/2fdv | HTTPS FTP |
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-Related structure data
Related structure data | 2fduC 2fdwC 2fdyC 1z10S 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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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 54671.637 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP2A6 / Plasmid: PCWORI / Production host: Escherichia coli (E. coli) / Strain (production host): DH-5 ALPHA / References: UniProt: P11509, unspecific monooxygenase |
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-Non-polymers , 5 types, 1457 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-HEM / #4: Chemical | ChemComp-D2G / #5: Chemical | ChemComp-EDO / #6: 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: 2.61 Å3/Da / Density % sol: 52.91 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Polyethylene Glycol2000, Monomethyl Ether, TRIS, AMMONIUM SULFATE, ANAPOE-X-405 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2005 Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing) |
Radiation | Monochromator: single crystal Si(311) bent monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→33.8 Å / Num. all: 294239 / Num. obs: 278644 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.045 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.662 / % possible all: 70.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1Z10 Resolution: 1.65→33.8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→33.8 Å
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Refine LS restraints |
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