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Yorodumi- PDB-5vcd: Crystal structure of the cysteine depleted CYP3A4 bound to glycerol -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vcd | ||||||
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Title | Crystal structure of the cysteine depleted CYP3A4 bound to glycerol | ||||||
Components | Cytochrome P450 3A4CYP3A4 | ||||||
Keywords | OXIDOREDUCTASE / cytochrome P450 / CYP3A4 / monooxygenase / cysteine mutation / glycerol | ||||||
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: 1.95 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 | 5vcd.cif.gz | 213.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vcd.ent.gz | 168.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vc/5vcd ftp://data.pdbj.org/pub/pdb/validation_reports/vc/5vcd | HTTPS FTP |
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-Related structure data
Related structure data | 5vc0C 5vccSC 5vceC 5vcgC 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: 55671.570 Da / Num. of mol.: 1 Mutation: fragment 3-22 deletion; C58A; C64M; C98A, C239T; C377A; C468S; C-terminal 4-His 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-GOL / #4: Water | ChemComp-HOH / | Sequence details | MA are the first two residues, fragment 3-22 deleted | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.9 % |
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Crystal grow | Temperature: 298 K / Method: microbatch / pH: 7.5 / Details: PEG4000 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 24, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→79.73 Å / Num. obs: 37249 / % possible obs: 99.8 % / Redundancy: 5.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.036 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.5 / CC1/2: 0.535 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5VCC Resolution: 1.95→60.663 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.38
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→60.663 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.9364 Å / Origin y: -23.5007 Å / Origin z: -14.5253 Å
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Refinement TLS group | Selection details: (chain A and resseq 26:611) |