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Yorodumi- PDB-2wd7: PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wd7 | ||||||
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Title | PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00066750 | ||||||
Components | (PTERIDINE REDUCTASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / DRUG DISCOVERY / TRYPANOSOMATIDS / PTERIDINE REDUCTASE / METHOTREXATE RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Robinson, D.A. / Wyatt, P.G. / Spinks, D. / Brenk, R. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening. Authors: Mpamhanga, C.P. / Spinks, D. / Tulloch, L.B. / Shanks, E.J. / Robinson, D.A. / Collie, I.T. / Fairlamb, A.H. / Wyatt, P.G. / Frearson, J.A. / Hunter, W.N. / Gilbert, I.H. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wd7.cif.gz | 218 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wd7.ent.gz | 174.9 KB | Display | PDB format |
PDBx/mmJSON format | 2wd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wd7_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 2wd7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2wd7_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 2wd7_validation.cif.gz | 64.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wd/2wd7 ftp://data.pdbj.org/pub/pdb/validation_reports/wd/2wd7 | HTTPS FTP |
-Related structure data
Related structure data | 2wd8C 3gn1C 3gn2C 2c7vS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 28498.441 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase | ||||||
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#2: Protein | Mass: 28514.441 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-VGD / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | pH: 4.5 / Details: 1.8M NA ACETATE, 0.1M CITRATE BUFFER PH6.0, pH 4.5 |
-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 IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 18, 2007 / 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→30 Å / Num. obs: 71041 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 63.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2C7V Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.254 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.143 / 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 / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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