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- PDB-7rkw: Naegleria fowleri CYP51(NfCYP51) complex with (S)-1-(4-fluorophen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rkw | ||||||
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Title | Naegleria fowleri CYP51(NfCYP51) complex with (S)-1-(4-fluorophenyl)-2-(1H-imidazol-1-yl)ethyl 3,5-dichlorobenzoate | ||||||
![]() | Protein CYP51 | ||||||
![]() | OXIDOREDUCTASE / ergosterol biosynthesis / Azole inhibitors | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sharma, V. / Podust, L.M. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.9 KB | Display | ![]() |
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PDB format | ![]() | 81.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 18.8 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rkrC ![]() 7rktC ![]() 5tl8S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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: 53559.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: NF0102700 / Plasmid: PCW-LIC / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-HEM / |
#3: Chemical | ChemComp-5TV / ( |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.69 % / 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; 3.18% 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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2021 / Details: MIRRORS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.81→70.94 Å / Num. obs: 40431 / % possible obs: 93.7 % / Redundancy: 6.069 % / Biso Wilson estimate: 55.33 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.00056 / Rrim(I) all: 0.00062 / Χ2: 0.901 / Net I/σ(I): 12.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5TL8 Resolution: 1.81→70.94 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.962 / SU B: 6.282 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.141 / 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: 128.08 Å2 / Biso mean: 60.927 Å2 / Biso min: 33.66 Å2
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Refinement step | Cycle: final / Resolution: 1.81→70.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.81→1.855 Å / Rfactor Rfree error: 0
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