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- PDB-4g7g: Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4g7g | ||||||
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Title | Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the VNI derivative (R)-N-(1-(3,4'-difluorobiphenyl-4-yl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadiazol-2-yl)benzamide [VNI/VNF (VFV)] | ||||||
![]() | sterol 14-alpha-demethylase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / cytochrome P450 fold / heme / monooxygenase / sterol biosynthesis / eukaryotic membrane biogenesis / cytochrome P450 reductase / endoplasmic reticulum membrane / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | ![]() membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity ...membrane biogenesis / sterol 14alpha-demethylase / sterol 14-demethylase activity / steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / sterol metabolic process / bile acid biosynthetic process / cholesterol homeostasis / nuclear envelope / oxidoreductase activity / iron ion binding / heme binding / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hargrove, T.Y. / Wawrzak, Z. / Waterman, M.R. / Lepesheva, G.I. | ||||||
![]() | ![]() Title: VFV as a New Effective CYP51 Structure-Derived Drug Candidate for Chagas Disease and Visceral Leishmaniasis. Authors: Lepesheva, G.I. / Hargrove, T.Y. / Rachakonda, G. / Wawrzak, Z. / Pomel, S. / Cojean, S. / Nde, P.N. / Nes, W.D. / Locuson, C.W. / Calcutt, M.W. / Waterman, M.R. / Daniels, J.S. / Loiseau, P.M. / Villalta, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 747.8 KB | Display | ![]() |
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PDB format | ![]() | 620.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 72.9 KB | Display | |
Data in CIF | ![]() | 97.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g3jC ![]() 3g1qS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50759.902 Da / Num. of mol.: 4 / Fragment: UNP residues 29-476 / Mutation: P29G, T30K, D31L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-VFV / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.63 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: potassium phosphate, sodium chloride, glycerol, PEG3350, N-tetradecyl-beta-D-maltoside, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2012 / Details: Be Lenses/Diamond Laue Mono |
Radiation | Monochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→29.817 Å / Num. all: 123297 / Num. obs: 120831 / % possible obs: 98 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 2.6 / Redundancy: 4.6 % / Biso Wilson estimate: 37.85 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5970 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3G1Q Resolution: 2.05→29.817 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.406 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT 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: 44.796 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→29.817 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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