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- PDB-2wd8: PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX W... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2wd8 | ||||||
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Title | PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00071204 | ||||||
![]() | PTERIDINE REDUCTASE![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Robinson, D.A. / Wyatt, P.G. / Spinks, D. / Brenk, R. | ||||||
![]() | ![]() 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. #1: ![]() Title: Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate. Authors: Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Tulloch, L.B. / Fyfe, P.K. / Mcluskey, K. / Fairlamb, A.H. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 216.4 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2wd7C ![]() 3gn1C ![]() 3gn2C ![]() 2c7vS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ![]() #3: Chemical | ![]() #4: Chemical | ChemComp-VGF / #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow![]() | pH: 4.6 / Details: 1.8M NA ACETATE, 0.1M CITRATE BUFFER PH6.0, pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 29, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→30 Å / Num. obs: 48991 / % possible obs: 84.7 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.4 / % possible all: 84.9 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2C7V Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.964 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.291 / ESU R Free: 0.218 / 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: 32.285 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→30 Å
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Refine LS restraints |
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