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Yorodumi- PDB-6t97: Trypanothione Reductase from Leismania infantum in complex with TRL190 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6t97 | ||||||
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Title | Trypanothione Reductase from Leismania infantum in complex with TRL190 | ||||||
Components | Trypanothione reductase | ||||||
Keywords | FLAVOPROTEIN / Inhibitor / Complex / Oxidoreductase / Leishmania / Drug | ||||||
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 / cellular response to oxidative stress / flavin adenine dinucleotide binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Leishmania infantum (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Carriles, A. / Hermoso, J.A. | ||||||
Funding support | Spain, 1items
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Citation | Journal: To Be Published Title: Scaffold hopping identifies new triazole-and triazolium-based inhibitors of Leishmania infantum Trypanothione Reductase with potent and selective antileishmanial activity Authors: Revuelto, A. / de Lucio, H. / Carriles, A. / Garcia Soriano, J.C. / Sanchez-Murcia, P.A. / Hermoso, J.A. / Gago, F. / Camarasa, M.J. / Jimenez-Ruiz, A. / Velazquez, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6t97.cif.gz | 212 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6t97.ent.gz | 167.8 KB | Display | PDB format |
PDBx/mmJSON format | 6t97.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/6t97 ftp://data.pdbj.org/pub/pdb/validation_reports/t9/6t97 | HTTPS FTP |
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-Related structure data
Related structure data | 2jk6S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 52868.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: TRYR, LINF_050008500, LINJ_05_0350 / Production host: Escherichia coli (E. coli) References: UniProt: A4HSF7, trypanothione-disulfide reductase |
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-Non-polymers , 5 types, 236 molecules
#2: Chemical | ChemComp-FAD / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-MWW / | #6: Water | ChemComp-HOH / | |
-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: 4.82 Å3/Da / Density % sol: 74.47 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.2M ammonium sulphate, 0.1M Tris-HCl pH 8-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→48.1 Å / Num. obs: 26273 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.035 / Rrim(I) all: 0.095 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.736 / Num. unique obs: 3759 / CC1/2: 0.943 / Rpim(I) all: 0.286 / Rrim(I) all: 0.791 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2JK6 Resolution: 2.8→48.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.812 / SU ML: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.298 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 153.02 Å2 / Biso mean: 65.685 Å2 / Biso min: 23.59 Å2
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Refinement step | Cycle: final / Resolution: 2.8→48.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.997 Å / Origin y: -1.204 Å / Origin z: -46.891 Å
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Refinement TLS group |
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