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Yorodumi- PDB-5esk: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5esk | |||||||||
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Title | Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) G464S mutant complexed with itraconazole | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / CYP51 / oxidoreductase-oxidoreductase inhibitor complex | |||||||||
Function / homology | Function and homology information ergosterol biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / methyltransferase activity / methylation / iron ion binding / heme binding / endoplasmic reticulum / membrane Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å | |||||||||
Authors | Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D.A. / Monk, B.C. | |||||||||
Funding support | New Zealand, 2items
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Citation | Journal: Antimicrob.Agents Chemother. / Year: 2018 Title: Impact of Homologous Resistance Mutations from Pathogenic Yeast on Saccharomyces cerevisiae Lanosterol 14 alpha-Demethylase. Authors: Sagatova, A.A. / Keniya, M.V. / Tyndall, J.D.A. / Monk, B.C. #1: Journal: Antimicrob. Agents Chemother. / Year: 2015 Title: Structural Insights into Binding of the Antifungal Drug Fluconazole to Saccharomyces cerevisiae Lanosterol 14alpha-Demethylase. Authors: Sagatova, A.A. / Keniya, M.V. / Wilson, R.K. / Monk, B.C. / Tyndall, J.D. #2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014 Title: Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Authors: Monk, B.C. / Tomasiak, T.M. / Keniya, M.V. / Huschmann, F.U. / Tyndall, J.D. / O'Connell, J.D. / Cannon, R.D. / McDonald, J.G. / Rodriguez, A. / Finer-Moore, J.S. / Stroud, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5esk.cif.gz | 127 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5esk.ent.gz | 95.4 KB | Display | PDB format |
PDBx/mmJSON format | 5esk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5esk_validation.pdf.gz | 973.4 KB | Display | wwPDB validaton report |
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Full document | 5esk_full_validation.pdf.gz | 983.1 KB | Display | |
Data in XML | 5esk_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 5esk_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/5esk ftp://data.pdbj.org/pub/pdb/validation_reports/es/5esk | HTTPS FTP |
-Related structure data
Related structure data | 5eseC 5esfC 5esgC 5eshC 5esiC 5esjC 4lxjS C: citing same article (ref.) 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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Unit cell |
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-Components
#1: Protein | Mass: 61915.238 Da / Num. of mol.: 1 / Mutation: G464S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2Delta / References: UniProt: A6ZSR0 |
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#2: Chemical | ChemComp-1YN / |
#3: Chemical | ChemComp-HEM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG-400 45%, 0.1 M glycine / PH range: 9.3-9.5 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.24→59.54 Å / Num. obs: 38314 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.24→2.31 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXJ Resolution: 2.24→50.662 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.92 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.24→50.662 Å
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Refine LS restraints |
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LS refinement shell |
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