+Open data
-Basic information
Entry | Database: PDB / ID: 4k9w | ||||||
---|---|---|---|---|---|---|---|
Title | Complex of human CYP3A4 with a desoxyritonavir analog | ||||||
Components | Cytochrome P450 3A4 | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cytochrome P450 3A4 / alpha-beta protein / cytochrome P450 fold / monooxygenase / cytochrome P450 reductase / endoplasmic reticulum / OXIDOREDUCTASE-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 metabolic process / androgen metabolic process / steroid hydroxylase activity / xenobiotic catabolic process / monooxygenase activity / steroid binding / xenobiotic metabolic process / cholesterol metabolic process / lipid metabolic process / oxygen binding / oxidoreductase activity / 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: 2.399 Å | ||||||
Authors | Sevrioukova, I.F. / Poulos, T.L. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: Dissecting Cytochrome P450 3A4-Ligand Interactions Using Ritonavir Analogues. Authors: Sevrioukova, I.F. / Poulos, T.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k9w.cif.gz | 749.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k9w.ent.gz | 628.8 KB | Display | PDB format |
PDBx/mmJSON format | 4k9w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4k9w_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4k9w_full_validation.pdf.gz | 2.8 MB | Display | |
Data in XML | 4k9w_validation.xml.gz | 69.7 KB | Display | |
Data in CIF | 4k9w_validation.cif.gz | 89.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k9/4k9w ftp://data.pdbj.org/pub/pdb/validation_reports/k9/4k9w | HTTPS FTP |
-Related structure data
Related structure data | 4k9tC 4k9uC 4k9vC 4k9xC 3nxuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
| ||||||||
Details | Monomeric assembly confirmed by gel filtration (Reference: Sevrioukova I.F. and Poulos T.L., PNAS 2010, 107, 18422-18427) |
-Components
#1: Protein | Mass: 55757.812 Da / Num. of mol.: 4 / Mutation: 3-22 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Strain: human / Gene: CYP3A3, CYP3A4 / 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 #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-7AW / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
---|---|
Crystal grow | Temperature: 298 K / Method: microbatch uinder oil / pH: 5.9 Details: PEG 3350, sodium malonate, pH 5.9, microbatch uinder oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 200 K | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2012 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
| |||||||||||||||
Reflection | Resolution: 2.399→51.5 Å / Num. all: 77051 / Num. obs: 73892 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.1 | |||||||||||||||
Reflection shell | Resolution: 2.399→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / % possible all: 91 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NXU Resolution: 2.399→47.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 13.651 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 60.429 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.399→47.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.399→2.461 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|