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- PDB-3q30: Human Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3q30 | ||||||
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Title | Human Squalene synthase in complex with (2R,3R)-2-Carboxymethoxy-3-[5-(2-naphthalenyl)pentyl]aminocarbonyl-3-[5-(2-naphthalenyl)pentyloxy]propionic acid | ||||||
![]() | Squalene synthase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / isoprene biosynthesis / lipid synthesis / multifunctional enzyme / oxidoreductase / steroid biosynthesis / sterol biosynthesis / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Suzuki, M. / Shimizu, H. / Katakura, S. / Yamazaki, K. / Higashihashi, N. / Ichikawa, M. / Yokomizo, A. / Itoh, M. / Sugita, K. / Usui, H. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.9 KB | Display | ![]() |
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PDB format | ![]() | 65.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3asxC ![]() 3q2zC ![]() 1ezfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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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.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-D61 / ( | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.33 % |
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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 |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 19, 2000 / 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→25 Å / Num. all: 25771 / Num. obs: 25771 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.59 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.53 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3 / Num. unique all: 2567 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EZF Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.922 / SU B: 4.015 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Although electron density peak corresponding to Arg52-Phe54 exist, this peptide region cannot be modeled to the shape of observed density. Possible cause of this failure is multiple ...Details: Although electron density peak corresponding to Arg52-Phe54 exist, this peptide region cannot be modeled to the shape of observed density. Possible cause of this failure is multiple conformation. There is a planer electron density peak possibly corresponding to the intrinsic lipid molecule between bound compound and Phe 54. Any atomic model for this density has not neen built.
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.838 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Total num. of bins used: 15
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