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Yorodumi- PDB-4ck9: STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ck9 | ||||||
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Title | STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (S)-1-(4-chlorophenyl)-2-(1H-imidazol-1-yl)ethyl 4- isopropylphenylcarbamate (LFT) | ||||||
Components | STEROL 14-ALPHA DEMETHYLASE | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME P450 / MONOOXYGENASE / STEROL BIOSYNTHESIS / EUKARYOTIC MEMBRANES / CYTOCHROME P450 FOLD / ENDOPLASMIC RETICULUM MEMBRANE | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol biosynthetic process / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.74 Å | ||||||
Authors | Friggeri, L. / Wawrzak, Z. / Tortorella, S. / Lepesheva, G.I. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Structural Basis for Rational Design of Inhibitors Targeting Trypanosoma Cruzi Sterol 14Alpha-Demethylase: Two Regions of the Enzyme Molecule Potentiate its Inhibition. Authors: Friggeri, L. / Hargrove, T.Y. / Rachakonda, G. / Williams, A.D. / Wawrzak, Z. / Di Santo, R. / De Vita, D. / Waterman, M.R. / Tortorella, S. / Villalta, F. / Lepesheva, G.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ck9.cif.gz | 196.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ck9.ent.gz | 157.1 KB | Display | PDB format |
PDBx/mmJSON format | 4ck9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ck9_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4ck9_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4ck9_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 4ck9_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ck9 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ck9 | HTTPS FTP |
-Related structure data
Related structure data | 4ck8C 4ckaC 4h6oS 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: 52552.898 Da / Num. of mol.: 1 / Fragment: RESIDUES 32-481 Source method: isolated from a genetically manipulated source Details: GENBANK AAW47718.1 / Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: THLAHUEN / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174 / References: UniProt: Q7Z1V1, sterol 14alpha-demethylase |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-LFT / ( |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE IS DESCRIBED IN LEPESHEVA ET AL. (2006) J. BIOL.CHEM., 281, P.3577 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | pH: 7.4 / Details: pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 30, 2013 / Details: BE LENSES DIAMOND LAUE |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→30 Å / Num. obs: 13383 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4H6O Resolution: 2.74→30 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.907 / SU B: 46.233 / SU ML: 0.404 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 90.516 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→30 Å
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