+Open data
-Basic information
Entry | Database: PDB / ID: 5vc0 | ||||||
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Title | Crystal structure of human CYP3A4 bound to ritonavir | ||||||
Components | Cytochrome P450 3A4CYP3A4 | ||||||
Keywords | OXIDOREDUCTASE/INHIBITOR / cytochrome P450 / CYP3A4 / monooxygenase / ritonavir / inhibitor / OXIDOREDUCTASE-INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Sevrioukova, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2017 Title: High-Level Production and Properties of the Cysteine-Depleted Cytochrome P450 3A4. Authors: Sevrioukova, I.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vc0.cif.gz | 212.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vc0.ent.gz | 169.6 KB | Display | PDB format |
PDBx/mmJSON format | 5vc0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/5vc0 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/5vc0 | HTTPS FTP |
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-Related structure data
Related structure data | 5vccC 5vcdC 5vceC 5vcgC 4k9wS 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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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: residue 3-22 deletion, C-terminal 4-histidine tag Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP3A4, CYP3A3 / Production host: Escherichia coli (E. coli) References: UniProt: P08684, EC: 1.14.13.157, EC: 1.14.13.32, EC: 1.14.13.67, kynurenine 3-monooxygenase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-RIT / |
Sequence details | MET ALA are the first two residues, the fragment 3-22 was deleted |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.82 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7.4 / Details: Hampton PegIon2 solution #15 |
-Data collection
Diffraction | Mean temperature: 107 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→78.17 Å / Num. obs: 13476 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.042 / Net I/av σ(I): 9.1 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 6 % / Rmerge(I) obs: 1.798 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1938 / CC1/2: 0.34 / Rpim(I) all: 0.79 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4k9w Resolution: 2.7→78.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.918 / SU B: 44.67 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 132.665 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→78.17 Å
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