[English] 日本語
Yorodumi- PDB-8pf3: Crystal structure of Trypanosoma brucei trypanothione reductase i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pf3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)(4-fluorophenyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium | ||||||
Components | Trypanothione reductase | ||||||
Keywords | OXIDOREDUCTASE / oxidoreductase activity / nucleotide binding / flavoenzyme / inhibitor binding | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Exertier, C. / Ilari, A. / Fiorillo, A. / Antonelli, L. | ||||||
Funding support | Italy, 1items
| ||||||
Citation | Journal: J.Med.Chem. / Year: 2024 Title: Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis. Authors: Exertier, C. / Salerno, A. / Antonelli, L. / Fiorillo, A. / Ocello, R. / Seghetti, F. / Caciolla, J. / Uliassi, E. / Masetti, M. / Fiorentino, E. / Orsini, S. / Di Muccio, T. / Ilari, A. / Bolognesi, M.L. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8pf3.cif.gz | 404.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8pf3.ent.gz | 328.3 KB | Display | PDB format |
PDBx/mmJSON format | 8pf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8pf3_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8pf3_full_validation.pdf.gz | 2.6 MB | Display | |
Data in XML | 8pf3_validation.xml.gz | 75.4 KB | Display | |
Data in CIF | 8pf3_validation.cif.gz | 104.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/8pf3 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/8pf3 | HTTPS FTP |
-Related structure data
Related structure data | 8pf4C 8pf5C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 53497.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Due to high flexibility of protein terminal parts, the electronic density being absent for the N- and C-terminal segment, we were not able to reconstruct the polypeptid chain for the initial ...Details: Due to high flexibility of protein terminal parts, the electronic density being absent for the N- and C-terminal segment, we were not able to reconstruct the polypeptid chain for the initial GS and the last DSNL residues. Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: DPX39_100110900 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A3L6KZJ1, trypanothione-disulfide reductase |
---|
-Non-polymers , 5 types, 608 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-YJ6 / Mass: 746.692 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H41Cl2F2N4O3 / Feature type: SUBJECT OF INVESTIGATION #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-IMD / | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.34 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 13-15% PEG3350, 22-24% MPD, 40 mM imidazole pH 7.5, 50 mM NaBr |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→168.54 Å / Num. obs: 117489 / % possible obs: 99.7 % / Redundancy: 6 % / CC1/2: 0.996 / Net I/σ(I): 10.37 |
Reflection shell | Resolution: 2.15→2.28 Å / Mean I/σ(I) obs: 2.25 / Num. unique obs: 18906 / CC1/2: 0.741 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→168.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.936 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 42.179 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.15→168.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|