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Yorodumi- PDB-3wsa: The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3wsa | ||||||
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Title | The Tuberculosis Drug SQ109 Inhibits Trypanosoma cruzi Cell Proliferation and acts Synergistically with Posaconazole | ||||||
Components | Squalene synthase | ||||||
Keywords | TRANSFERASE / isoprenoids / drug discovery / human squalene synthase / SQ-109 | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shang, N. / Li, Q. / Huang, C.H. / Oldfield, E. / Guo, R.T. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 Title: SQ109, a new drug lead for Chagas disease. Authors: Veiga-Santos, P. / Li, K. / Lameira, L. / de Carvalho, T.M. / Huang, G. / Galizzi, M. / Shang, N. / Li, Q. / Gonzalez-Pacanowska, D. / Hernandez-Rodriguez, V. / Benaim, G. / Guo, R.T. / ...Authors: Veiga-Santos, P. / Li, K. / Lameira, L. / de Carvalho, T.M. / Huang, G. / Galizzi, M. / Shang, N. / Li, Q. / Gonzalez-Pacanowska, D. / Hernandez-Rodriguez, V. / Benaim, G. / Guo, R.T. / Urbina, J.A. / Docampo, R. / de Souza, W. / Oldfield, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3wsa.cif.gz | 397.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3wsa.ent.gz | 327.7 KB | Display | PDB format |
PDBx/mmJSON format | 3wsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3wsa_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3wsa_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 3wsa_validation.xml.gz | 76.6 KB | Display | |
Data in CIF | 3wsa_validation.cif.gz | 100.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ws/3wsa ftp://data.pdbj.org/pub/pdb/validation_reports/ws/3wsa | HTTPS FTP |
-Related structure data
Related structure data | 1ezfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 41288.988 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 31-370 / Mutation: K248L, K315L, K318L 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-RWZ / #3: Water | ChemComp-HOH / | Sequence details | THE EXPERIMENT | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.5 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.2 Details: 0.2M sodium citrate, pH 8.2, 28% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.9→25 Å / Num. obs: 48462 / % possible obs: 93.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.8 / Num. unique all: 16426 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EZF Resolution: 2.9→25 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.9→25 Å
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LS refinement shell | Resolution: 2.9→3 Å / Rfactor Rfree: 0.33 / Rfactor Rwork: 0.313 |