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Yorodumi- PDB-4i3q: Crystal structure of human CYP3A4 coordinated to a water molecule -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i3q | ||||||
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Title | Crystal structure of human CYP3A4 coordinated to a water molecule | ||||||
Components | Cytochrome P450 3A4CYP3A4 | ||||||
Keywords | OXIDOREDUCTASE / hemoprotein / monooxygenase / cytochrome P450 reductase / cytochrome b5 / endoplasmic reticulum / cytochrome P450 | ||||||
Function / homology | Function and homology information quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process ...quinine 3-monooxygenase / 1,8-cineole 2-exo-monooxygenase / albendazole monooxygenase (sulfoxide-forming) / quinine 3-monooxygenase activity / 1,8-cineole 2-exo-monooxygenase activity / 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity / vitamin D3 25-hydroxylase activity / testosterone 6-beta-hydroxylase activity / vitamin D 24-hydroxylase activity / vitamin D catabolic process / retinoic acid 4-hydroxylase activity / aflatoxin metabolic process / caffeine oxidase activity / estrogen 16-alpha-hydroxylase activity / estrogen 2-hydroxylase activity / lipid hydroxylation / anandamide 8,9 epoxidase activity / anandamide 11,12 epoxidase activity / anandamide 14,15 epoxidase activity / alkaloid catabolic process / Aflatoxin activation and detoxification / Biosynthesis of maresin-like SPMs / monoterpenoid metabolic process / vitamin D metabolic process / Atorvastatin ADME / : / oxidative demethylation / steroid catabolic process / Xenobiotics / Phase I - Functionalization of compounds / long-chain fatty acid biosynthetic process / estrogen metabolic process / retinol metabolic process / retinoic acid metabolic process / Prednisone ADME / unspecific monooxygenase / aromatase activity / Aspirin ADME / steroid hydroxylase activity / steroid metabolic process / androgen metabolic process / xenobiotic catabolic process / steroid binding / xenobiotic metabolic process / cholesterol metabolic process / monooxygenase activity / lipid metabolic process / oxygen binding / oxidoreductase activity / 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 / PHASER / Resolution: 2.602 Å | ||||||
Authors | Sevrioukova, I.F. / Poulos, T.L. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Pyridine-Substituted Desoxyritonavir Is a More Potent Inhibitor of Cytochrome P450 3A4 than Ritonavir. Authors: Sevrioukova, I.F. / Poulos, T.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i3q.cif.gz | 208.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i3q.ent.gz | 167.7 KB | Display | PDB format |
PDBx/mmJSON format | 4i3q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/4i3q ftp://data.pdbj.org/pub/pdb/validation_reports/i3/4i3q | HTTPS FTP |
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-Related structure data
Related structure data | 4i4gC 4i4hC 1woeS 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 55757.812 Da / Num. of mol.: 1 / Mutation: residues 3-22 deleted Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A4, CYP3A3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P08684, 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 ...References: UniProt: P08684, 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, EC: 1.14.13.157, EC: 1.14.13.32, EC: 1.14.13.67, EC: 1.14.13.97 |
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#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Sequence details | THIS PROTEIN CONSISTS OF UNP RESIDUES 1-2 AND 23-503. DUE TO A DELETION OF UNP RESIDUES 3-22, ...THIS PROTEIN CONSISTS OF UNP RESIDUES 1-2 AND 23-503. DUE TO A DELETION OF UNP RESIDUES 3-22, RESIDUES 21-22 (MET ALA) CORRESPOND |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.64 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 6 Details: PEG 3350, sodium malonate, pH 6.0, microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2012 / Details: mirrors |
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.127 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→65.3 Å / Num. all: 16524 / Num. obs: 16260 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.516 / Mean I/σ(I) obs: 2.3 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB ENTRY 1WOE Resolution: 2.602→65.27 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 35.644 / SU ML: 0.343 / Cross valid method: THROUGHOUT / ESU R: 2.329 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 93.672 Å2
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Refinement step | Cycle: LAST / Resolution: 2.602→65.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.602→2.669 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 19.7251 Å / Origin y: 23.9985 Å / Origin z: -13.4491 Å
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