[English] 日本語
Yorodumi- PDB-4enh: Crystal Structure of Human Cytochrome P450 CYP46A1 with Fluvoxami... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4enh | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human Cytochrome P450 CYP46A1 with Fluvoxamine Bound | ||||||
Components | Cholesterol 24-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / enzyme / P450 / fluvoxamine / endoplasmic reticulum | ||||||
Function / homology | Function and homology information cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity ...cholesterol 24-hydroxylase / cholesterol 24-hydroxylase activity / protein localization to membrane raft / testosterone 16-beta-hydroxylase activity / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / progesterone metabolic process / sterol metabolic process / bile acid biosynthetic process / regulation of long-term synaptic potentiation / steroid hydroxylase activity / cholesterol catabolic process / Endogenous sterols / xenobiotic metabolic process / presynapse / nervous system development / postsynapse / iron ion binding / dendrite / heme binding / endoplasmic reticulum membrane / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Stout, C.D. / Mast, N. / Pikuleva, I.A. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2012 Title: In Silico and Intuitive Predictions of CYP46A1 Inhibition by Marketed Drugs with Subsequent Enzyme Crystallization in Complex with Fluvoxamine. Authors: Mast, N. / Linger, M. / Clark, M. / Wiseman, J. / Stout, C.D. / Pikuleva, I.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4enh.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4enh.ent.gz | 79.3 KB | Display | PDB format |
PDBx/mmJSON format | 4enh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/en/4enh ftp://data.pdbj.org/pub/pdb/validation_reports/en/4enh | HTTPS FTP |
---|
-Related structure data
Related structure data | 2q9fS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 52125.086 Da / Num. of mol.: 1 / Fragment: UNP residues 51-500 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CYP46A1, CYP46 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: Q9Y6A2, EC: 1.14.13.98 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-FVX / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
---|---|
Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: Crystals were grown after mixing 1 ul of an ~40 mg/ml P450 solution with 1 ul of precipitant solution (15% PEG 8000, 50 M FLX, 50 mM potassium phosphate, 20% glycerol), pH 5.8, VAPOR ...Details: Crystals were grown after mixing 1 ul of an ~40 mg/ml P450 solution with 1 ul of precipitant solution (15% PEG 8000, 50 M FLX, 50 mM potassium phosphate, 20% glycerol), pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.09717 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.09717 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→92.129 Å / Num. obs: 18625 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.3 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2Q9F Resolution: 2.5→60.57 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.884 / WRfactor Rfree: 0.2833 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9093 / SU B: 6.642 / SU ML: 0.143 / SU R Cruickshank DPI: 0.1228 / SU Rfree: 0.0666 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.8 Å2 / Biso mean: 44.5623 Å2 / Biso min: 11.96 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→60.57 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
|