[English] 日本語
Yorodumi- PDB-5ajr: Sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ajr | ||||||
---|---|---|---|---|---|---|---|
Title | Sterol 14-alpha demethylase (CYP51) from Trypanosoma cruzi in complex with the 1-tetrazole derivative VT-1161 ((R)-2-(2,4-Difluorophenyl)-1, 1-difluoro-3-(1H-tetrazol-1-yl)-1-(5-(4-(2,2,2-trifluoroethoxy)phenyl) pyridin-2-yl)propan-2-ol) | ||||||
Components | STEROL 14-ALPHA DEMETHYLASE | ||||||
Keywords | OXIDOREDUCTASE / CYTOCHROME P450 / CYP51 / 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: 2.75 Å | ||||||
Authors | Wawrzak, Z. / Hoekstra, W. / I Lepesheva, G. | ||||||
Citation | Journal: Antimicrob.Agents Chemother. / Year: 2015 Title: Clinical Candidate Vt-1161'S Antiparasitic Effect in Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme Cyp51 from Trypanosoma Cruzi. Authors: Hoekstra, W.J. / Hargrove, T.Y. / Wawrzak, Z. / Da Gama Jaen Batista, D. / Da Silva, C.F. / Nefertiti, A.S.G. / Rachakonda, G. / Schotzinger, R.J. / Villalta, F. / Soeiro, M.D.N.C. / Lepesheva, G.I. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ajr.cif.gz | 106.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ajr.ent.gz | 80.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ajr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ajr_validation.pdf.gz | 1004.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ajr_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5ajr_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 5ajr_validation.cif.gz | 30.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5ajr ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5ajr | HTTPS FTP |
-Related structure data
Related structure data | 3zg2S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 52552.898 Da / Num. of mol.: 1 / Fragment: 29-481 Source method: isolated from a genetically manipulated source 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 | ChemComp-HEM / |
#3: Chemical | ChemComp-VT1 / ( |
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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.9 % / Description: NONE |
---|---|
Crystal grow | pH: 7.4 / Details: pH 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 22, 2014 / 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: 2.75→54.61 Å / Num. obs: 14063 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.75→2.82 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 3.5 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZG2 Resolution: 2.75→54.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.934 / SU B: 22.421 / SU ML: 0.418 / Cross valid method: THROUGHOUT / ESU R Free: 0.404 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 117.897 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→54.61 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|