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- PDB-2wpf: Trypanosoma brucei trypanothione reductase in complex with 3,4- d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wpf | ||||||
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Title | Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00085762) | ||||||
![]() | TRYPANOTHIONE REDUCTASE | ||||||
![]() | OXIDOREDUCTASE / TRYPANOSOMIASIS / SLEEPING SICKNESS / FLAVOPROTEIN / REDOX-ACTIVE CENTER | ||||||
Function / homology | ![]() trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / nucleoplasm / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Alphey, M.S. / Patterson, S. / Fairlamb, A.H. | ||||||
![]() | ![]() Title: Dihydroquinazolines as a Novel Class of Trypanosoma Brucei Trypanothione Reductase Inhibitors: Discovery, Synthesis, and Characterization of Their Binding Mode by Protein Crystallography. Authors: Patterson, S. / Alphey, M.S. / Jones, D.C. / Shanks, E.J. / Street, I.P. / Frearson, J.A. / Wyatt, P.G. / Gilbert, I.H. / Fairlamb, A.H. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 410.4 KB | Display | ![]() |
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PDB format | ![]() | 333.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
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Full document | ![]() | 2.6 MB | Display | |
Data in XML | ![]() | 88.1 KB | Display | |
Data in CIF | ![]() | 124.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2woiSC ![]() 2wovC ![]() 2wowC ![]() 2wp5C ![]() 2wp6C ![]() 2wpcC ![]() 2wpeC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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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 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P39051, UniProt: Q389T8*PLUS, trypanothione-disulfide reductase |
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-Non-polymers , 5 types, 1311 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/WPF.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/WPF.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/BR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-WPF / #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.39 % / Description: NONE |
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Crystal grow | pH: 8 Details: 15MG/ML PROTEIN IN 25MM HEPES PH 7.5, 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG 3350, 40MM IMIDAZOLE PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 9, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→19.9 Å / Num. obs: 160960 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.9→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2WOI Resolution: 1.9→19.888 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.39 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.316 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.888 Å
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Refine LS restraints |
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