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Yorodumi- PDB-4ck8: STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMP... -
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-Basic information
Entry | Database: PDB / ID: 4ck8 | ||||||
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Title | STEROL 14-ALPHA DEMETHYLASE (CYP51)FROM TRYPANOSOMA CRUZI IN COMPLEX WITH (R)-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl 4-(4-(3,4- dichlorophenyl)piperazin-1-yl)phenylcarbamate (LFD) | ||||||
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 steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol 14alpha-demethylase / sterol 14-demethylase 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: 2.62 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 | 4ck8.cif.gz | 384 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ck8.ent.gz | 312.9 KB | Display | PDB format |
PDBx/mmJSON format | 4ck8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ck8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4ck8_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4ck8_validation.xml.gz | 45.4 KB | Display | |
Data in CIF | 4ck8_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/4ck8 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/4ck8 | HTTPS FTP |
-Related structure data
Related structure data | 4ck9C 4ckaC 3zg2S 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 52552.898 Da / Num. of mol.: 2 / 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 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE IS DESCRIBED IN LEPESHEVA ET AL. (2006) J. BIOL.CHEM., 281, P.3577 | |
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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: 2.95 Å3/Da / Density % sol: 58 % / 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: 0.9787 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Nov 24, 2013 / Details: BE LENSES DIAMOND LAUE |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→30 Å / Num. obs: 36336 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 7.2 % / Biso Wilson estimate: 46.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 2.61→2.67 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.9 / % possible all: 99 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZG2 Resolution: 2.62→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.895 / SU B: 35.758 / SU ML: 0.329 / Cross valid method: THROUGHOUT / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 mean: 69.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2.62→30 Å
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