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Yorodumi- PDB-4coh: Crystal structure of Trypanosoma cruzi CYP51 bound to the sulfona... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4coh | ||||||
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Title | Crystal structure of Trypanosoma cruzi CYP51 bound to the sulfonamide derivative of the 4-aminopyridyl-based inhibitor | ||||||
Components | STEROL 14-ALPHA DEMETHYLASE | ||||||
Keywords | TRANSFERASE / CYP51 / STEROL 14-DEMETHYLASE / STEROL BIOSYNTHESIS / CHAGAS DISEASE | ||||||
Function / homology | Function and homology information sterol 14alpha-demethylase / sterol 14-demethylase activity / sterol biosynthetic process / iron ion binding / heme binding / membrane Similarity search - Function | ||||||
Biological species | TRYPANOSOMA CRUZI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å | ||||||
Authors | Vieira, D.F. / Choi, J.Y. / Roush, W.R. / Podust, L.M. | ||||||
Citation | Journal: Chembiochem / Year: 2014 Title: Expanding the Binding Envelope of Cyp51 Inhibitors Targeting Trypanosoma Cruzi with 4-Aminopyridyl-Based Sulfonamide Derivatives Authors: Vieira, D.F. / Choi, J.Y. / Roush, W.R. / Podust, L.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4coh.cif.gz | 208.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4coh.ent.gz | 164.1 KB | Display | PDB format |
PDBx/mmJSON format | 4coh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4coh_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 4coh_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4coh_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 4coh_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/4coh ftp://data.pdbj.org/pub/pdb/validation_reports/co/4coh | HTTPS FTP |
-Related structure data
Related structure data | 2wx2S 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: 53600.125 Da / Num. of mol.: 2 / Fragment: RESIDUES 29-481 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Plasmid: PCW / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): HMS174(DE3) References: UniProt: Q5I4E1, UniProt: Q7Z1V1*PLUS, sterol 14alpha-demethylase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | FIRST 28 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGKL SEQUENCE, 6XHIS TAG ...FIRST 28 RESIDUES AT THE N-TERMINUS ARE REPLACED WITH THE MAKKTSSKGK | |
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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: 2.42 Å3/Da / Density % sol: 49.3 % / Description: NONE |
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Crystal grow | pH: 7 / Details: 0.05 M AMMONIUM CITRATE, PH 7.0; 14% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 22, 2012 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→137.36 Å / Num. obs: 60841 / % possible obs: 95.6 % / Observed criterion σ(I): 1.5 / Redundancy: 7.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2.08→2.19 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 1.8 / % possible all: 76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WX2 Resolution: 2.08→137.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.784 / SU ML: 0.128 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.071 Å2
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Refinement step | Cycle: LAST / Resolution: 2.08→137.11 Å
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Refine LS restraints |
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