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Yorodumi- PDB-7rkr: Naegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(4-fluorophe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rkr | ||||||
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Title | Naegleria fowleri CYP51 (NfCYP51) complex with (S)-1-(4-fluorophenyl)-2-(1H-imidazol-1-yl)ethyl 3-(trifluoromethyl)benzoate | ||||||
Components | Protein CYP51 | ||||||
Keywords | OXIDOREDUCTASE / ergosterol biosynthesis / Azole inhibitors | ||||||
Function / homology | Function and homology information steroid 7-alpha-hydroxylase activity / oxysterol 7-alpha-hydroxylase activity / bile acid biosynthetic process / cholesterol homeostasis / iron ion binding / heme binding Similarity search - Function | ||||||
Biological species | Naegleria fowleri (brain-eating amoeba) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Sharma, V. / Podust, L.M. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2023 Title: Miconazole-like Scaffold is a Promising Lead for Naegleria fowleri -Specific CYP51 Inhibitors. Authors: Sharma, V. / Madia, V.N. / Tudino, V. / Nguyen, J.V. / Debnath, A. / Messore, A. / Ialongo, D. / Patacchini, E. / Palenca, I. / Basili Franzin, S. / Seguella, L. / Esposito, G. / Petrucci, R. ...Authors: Sharma, V. / Madia, V.N. / Tudino, V. / Nguyen, J.V. / Debnath, A. / Messore, A. / Ialongo, D. / Patacchini, E. / Palenca, I. / Basili Franzin, S. / Seguella, L. / Esposito, G. / Petrucci, R. / Di Matteo, P. / Bortolami, M. / Saccoliti, F. / Di Santo, R. / Scipione, L. / Costi, 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 | 7rkr.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rkr.ent.gz | 81.8 KB | Display | PDB format |
PDBx/mmJSON format | 7rkr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rkr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7rkr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7rkr_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 7rkr_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rk/7rkr ftp://data.pdbj.org/pub/pdb/validation_reports/rk/7rkr | HTTPS FTP |
-Related structure data
Related structure data | 7rktC 7rkwC 5tl8S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 53559.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria fowleri (brain-eating amoeba) Gene: NF0102700 / Plasmid: PCW-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: A0A2H4A2U9 | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-L49 / ( | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % / Description: Red elongated crystals of 0.3 mm size. |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 30 mM Calcium chloride; 4.50% v/v Jefframine M-600 pH-7.0; 33% v/v Polyethylene glycol monomethyl ether 550; 100 mM Bis-Tris Propane pH-7.0 |
-Data collection
Diffraction | Mean temperature: 110 K / Ambient temp details: Liquid Nitrogen flow / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2020 / Details: MIRROR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.1159 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.76→70.38 Å / Num. obs: 45818 / % possible obs: 98.1 % / Redundancy: 6.421 % / Biso Wilson estimate: 46.872 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.00096 / Rrim(I) all: 0.00104 / Χ2: 0.834 / Net I/σ(I): 8.94 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5TL8 Resolution: 1.76→70.38 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.284 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.127 / 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 max: 114.52 Å2 / Biso mean: 48.165 Å2 / Biso min: 24.77 Å2
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Refinement step | Cycle: final / Resolution: 1.76→70.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.801 Å / Rfactor Rfree error: 0
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