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Yorodumi- PDB-8wtr: HUMAN SQUALENE SYNTHASE IN COMPLEX WITH (1S,3R)-3-[2-Chloro-5-(2,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wtr | ||||||
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Title | HUMAN SQUALENE SYNTHASE IN COMPLEX WITH (1S,3R)-3-[2-Chloro-5-(2,2-dimethyl-propyl)-13-(2-methoxy-phenyl)-6,8-dioxo-5,6,7,8,10,11-hexahydro-13H-12-oxa-5,9-diaza-benzocycloundecen-9-yl]-cyclohexanecarboxylic acid | ||||||
Components | Squalene synthase | ||||||
Keywords | TRANSFERASE / TERPENOID SYNTHASE FOLD / 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 / ergosterol biosynthetic process / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) ...squalene synthase / farnesyl-diphosphate farnesyltransferase activity / farnesyl diphosphate metabolic process / squalene synthase activity / Cholesterol biosynthesis / farnesyltranstransferase activity / steroid biosynthetic process / ergosterol 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 | Suzuki, M. / Haginoya, N. / Suzuki, M. / Ishigai, Y. / Terayama, K. / Kanda, A. / Sugita, K. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Discovery of Novel 11-Membered Templates as Squalene Synthase Inhibitors. Authors: Haginoya, N. / Suzuki, M. / Suzuki, M. / Ishigai, Y. / Terayama, K. / Kanda, A. / Sugita, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wtr.cif.gz | 90 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wtr.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 8wtr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wtr_validation.pdf.gz | 818.7 KB | Display | wwPDB validaton report |
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Full document | 8wtr_full_validation.pdf.gz | 819.3 KB | Display | |
Data in XML | 8wtr_validation.xml.gz | 17 KB | Display | |
Data in CIF | 8wtr_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/8wtr ftp://data.pdbj.org/pub/pdb/validation_reports/wt/8wtr | HTTPS FTP |
-Related structure data
Related structure data | 8wtqC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 39166.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FDFT1 / Plasmid: PA-426 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS / References: UniProt: P37268, squalene synthase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-KV3 / ( Mass: 571.104 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H39ClN2O6 / Feature type: SUBJECT OF INVESTIGATION |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.92 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% PEG8000/ 50mM KH2PO4/ 1mM DTT. Complex crystal was prepared by soaking in 20% PEG8000/ 50mM KH2PO4, pH 6/ 1mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 1, 2003 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: confocal mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→38.23 Å / Num. obs: 26854 / % possible obs: 99.9 % / Redundancy: 3.53 % / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.074 / Χ2: 1.12 / Net I/σ(I): 7.5 / Num. measured all: 95599 / Scaling rejects: 719 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 3.597 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.157 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 81.6 Å2 / Biso mean: 18.952 Å2 / Biso min: 6.18 Å2
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Refinement step | Cycle: final / Resolution: 2→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.07 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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