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Yorodumi- PDB-2wpe: Trypanosoma brucei trypanothione reductase in complex with 3,4- d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wpe | ||||||
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Title | Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00073359) | ||||||
Components | TRYPANOTHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / TRYPANOSOMIASIS / SLEEPING SICKNESS / REDOX-ACTIVE CENTER | ||||||
Function / homology | Function and homology information trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / cell redox homeostasis / flavin adenine dinucleotide binding / nucleoplasm / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | TRYPANOSOMA BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Alphey, M.S. / Patterson, S. / Fairlamb, A.H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wpe.cif.gz | 412.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wpe.ent.gz | 334.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wpe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wpe_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 2wpe_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 2wpe_validation.xml.gz | 86.3 KB | Display | |
Data in CIF | 2wpe_validation.cif.gz | 122.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpe ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpe | HTTPS FTP |
-Related structure data
Related structure data | 2woiSC 2wovC 2wowC 2wp5C 2wp6C 2wpcC 2wpfC C: citing same article (ref.) 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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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.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: TREU927 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): CODONPLUS RIL References: UniProt: Q389T8, trypanothione-disulfide reductase |
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-Non-polymers , 7 types, 1248 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-WPE / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-MPD / ( | #7: Chemical | ChemComp-MRD / ( | #8: Water | ChemComp-HOH / | |
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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: 2.45 Å3/Da / Density % sol: 49.74 % / Description: NONE |
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Crystal grow | pH: 8 Details: 15MG/ML PROTEIN IN 25MM HEPES PH 7.5 AND 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG3350 AND 40MM IMIDAZOLE PH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 25, 2008 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46 Å / Num. obs: 123374 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.2 / % possible all: 87.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOI Resolution: 2.1→45.979 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.677 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.184 / 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: 27.723 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→45.979 Å
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Refine LS restraints |
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