+Open data
-Basic information
Entry | Database: PDB / ID: 2wov | ||||||
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Title | Trypanosoma brucei trypanothione reductase with bound NADP. | ||||||
Components | TRYPANOTHIONE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / TRYPANOSOMIASIS / SLEEPING SICKNESS / FLAVOPROTEIN / TRYPANOTHIONE / REDUCTASE / REDOX-ACTIVE CENTER | ||||||
Function / homology | Function and homology information 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 | TRYPANOSOMA BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Alphey, M.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 | 2wov.cif.gz | 393.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wov.ent.gz | 320.1 KB | Display | PDB format |
PDBx/mmJSON format | 2wov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wov_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 2wov_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 2wov_validation.xml.gz | 76.6 KB | Display | |
Data in CIF | 2wov_validation.cif.gz | 102.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wo/2wov ftp://data.pdbj.org/pub/pdb/validation_reports/wo/2wov | HTTPS FTP |
-Related structure data
Related structure data | 2woiSC 2wowC 2wp5C 2wp6C 2wpcC 2wpeC 2wpfC S: Starting model for refinement C: citing same article (ref.) |
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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
#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 #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-FAD / #4: Chemical | ChemComp-NA / #5: 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: 2.52 Å3/Da / Density % sol: 51.2 % / Description: NONE |
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Crystal grow | 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 13, 2009 / 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: 2.5→19.9 Å / Num. obs: 72546 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.6 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WOI Resolution: 2.5→19.847 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.891 / SU B: 9.955 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.73 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SOME RESIDUES AT N- AND C-TERMINI WERE MODELLED AS ALANINES OR OMITTED FROM THE MODEL DUE TO THEIR FLEXIBILITY AND POOR ELECTRON DENSITY
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Solvent computation | Ion probe radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.915 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→19.847 Å
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Refine LS restraints |
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