[English] 日本語
Yorodumi- PDB-3asx: Human Squalene synthase in complex with 1-{4-[{4-chloro-2-[(2-chl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3asx | ||||||
---|---|---|---|---|---|---|---|
Title | Human Squalene synthase in complex with 1-{4-[{4-chloro-2-[(2-chlorophenyl)(hydroxy)methyl]phenyl}(2,2-dimethylpropyl)amino]-4-oxobutanoyl}piperidine-3-carboxylic acid | ||||||
Components | Squalene synthase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / isoprene biosynthesis / lipid synthesis / multifunctional enzyme / oxidoreductase / steroid biosynthesis / sterol biosynthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression ...squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / PPARA activates gene expression / endoplasmic reticulum membrane / endoplasmic reticulum / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Shimizu, H. / Suzuki, M. / Katakura, S. / Yamazaki, K. / Higashihashi, N. / Ichikawa, M. / Yokomizo, A. / Itoh, M. / Sugita, K. / Usui, H. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2011 Title: Discovery of a new 2-aminobenzhydrol template for highly potent squalene synthase inhibitors Authors: Ichikawa, M. / Yokomizo, A. / Itoh, M. / Sugita, K. / Usui, H. / Shimizu, H. / Suzuki, M. / Terayama, K. / Kanda, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3asx.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3asx.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 3asx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3asx_validation.pdf.gz | 756.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3asx_full_validation.pdf.gz | 761.7 KB | Display | |
Data in XML | 3asx_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3asx_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/3asx ftp://data.pdbj.org/pub/pdb/validation_reports/as/3asx | HTTPS FTP |
-Related structure data
Related structure data | 3q2zC 3q30C 1ezfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 39166.699 Da / Num. of mol.: 1 / Fragment: UNP residues 31-370 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Production host: Escherichia coli (E. coli) / References: UniProt: P37268, squalene synthase |
---|---|
#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-D99 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.56 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: seeding method, pH 5, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 23, 2002 / Details: monochromator |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2→76.7 Å / Num. all: 26043 / Num. obs: 26043 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 27.188 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2→2.15 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3 / Num. unique all: 4085 / % possible all: 99.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EZF Resolution: 2→76.7 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 3.553 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 27.945 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→76.7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|