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Yorodumi- PDB-5s9y: PanDDA analysis group deposition -- Crystal Structure of Trypanos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5s9y | |||||||||
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Title | PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z24758179 | |||||||||
Components | N(1),N(8)-bis(glutathionyl)spermidine reductase | |||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE inhibitor / Diamond I04-1 fragment screening / PanDDA / XChemExplorer / OXIDOREDUCTASE-OXIDOREDUCTASE inhibitor complex | |||||||||
Function / homology | Function and homology information trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | Trypanosoma brucei (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.75 Å | |||||||||
Authors | Fiorillo, A. / Ilari, A. | |||||||||
Funding support | European Union, Italy, 2items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Innovative Approach for a Classic Target: Fragment Screening on Trypanothione Reductase Reveals New Opportunities for Drug Design. Authors: Fiorillo, A. / Colotti, G. / Exertier, C. / Liuzzi, A. / Seghetti, F. / Salerno, A. / Caciolla, J. / Ilari, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5s9y.cif.gz | 209.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5s9y.ent.gz | 168.4 KB | Display | PDB format |
PDBx/mmJSON format | 5s9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5s9y_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5s9y_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5s9y_validation.xml.gz | 41.5 KB | Display | |
Data in CIF | 5s9y_validation.cif.gz | 60.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/5s9y ftp://data.pdbj.org/pub/pdb/validation_reports/s9/5s9y | HTTPS FTP |
-Group deposition
ID | G_1002197 (12 entries) |
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Title | PanDDA analysis group deposition |
Type | changed state |
Description | Trypanosoma brucei Trypanothione Reductase screened against the DSiP Fragment Library by X-ray Crystallography at the XChem facility of Diamond Light Source beamline I04-1 |
-Related structure data
Related structure data | 6rb5S S: Starting model for refinement |
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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
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 53497.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Production host: Escherichia coli (E. coli) References: UniProt: A0A3L6KZJ1, trypanothione-disulfide reductase |
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-Non-polymers , 6 types, 543 molecules
#2: Chemical | #3: Chemical | ChemComp-DMS / #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-BR / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.26 Å3/Da / Density % sol: 45.66 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9126 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→64.24 Å / Num. obs: 98469 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.073 / Net I/σ(I): 13.6 / Num. measured all: 662683 / Scaling rejects: 1 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 6RB5 Resolution: 1.75→64.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.186 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.126 / 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: 103.55 Å2 / Biso mean: 38.681 Å2 / Biso min: 18.67 Å2
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Refinement step | Cycle: final / Resolution: 1.75→64.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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