[English] 日本語
Yorodumi- PDB-5esh: Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5esh | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Saccharomyces cerevisiae CYP51 (Lanosterol 14-alpha demethylase) G73W mutant in complex with itraconazole | |||||||||
Components | Lanosterol 14-alpha demethylase | |||||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / CYP51 / mutation / 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: 2.15 Å | |||||||||
Authors | Sagatova, A. / Keniya, M.V. / Wilson, R.K. / Sabherwal, M. / Tyndall, J.D.A. / Monk, B.C. | |||||||||
Funding support | New Zealand, 2items
| |||||||||
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: 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. #2: 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. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5esh.cif.gz | 128.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5esh.ent.gz | 96.3 KB | Display | PDB format |
PDBx/mmJSON format | 5esh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5esh_validation.pdf.gz | 985.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5esh_full_validation.pdf.gz | 988.7 KB | Display | |
Data in XML | 5esh_validation.xml.gz | 22 KB | Display | |
Data in CIF | 5esh_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/es/5esh ftp://data.pdbj.org/pub/pdb/validation_reports/es/5esh | HTTPS FTP |
-Related structure data
Related structure data | 5eseC 5esfC 5esgC 5esiC 5esjC 5eskC 4lxjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 62014.371 Da / Num. of mol.: 1 / Mutation: G73W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: YJM789 / Gene: ERG11, SCY_2394 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD2delta / References: UniProt: A6ZSR0, sterol 14alpha-demethylase |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-1YN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.23 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 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: 2.15→80.02 Å / Num. obs: 44569 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 2 / % possible all: 99.2 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LXJ Resolution: 2.15→29.949 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.13 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→29.949 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|