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- PDB-3jq8: Crystal structure of pteridine reductase 1 (PTR1) from Trypanosom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3jq8 | |||||||||
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Title | Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 6,7,7-trimethyl-7,8-dihydropteridine-2,4-diamine (DX3) | |||||||||
![]() | (Pteridine reductase ...) x 2 | |||||||||
![]() | OXIDOREDUCTASE / PTERIDINE REDUCTASE / PTR1 / TRYPANOSOMA BRUCEI / SHORT CHAIN DEHYDROGENASE / INHIBITOR | |||||||||
Function / homology | ![]() pteridine reductase / pteridine reductase activity / oxidoreductase activity / nucleotide binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Tulloch, L.B. / Hunter, W.N. | |||||||||
![]() | ![]() Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases. Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / 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 | ![]() | 230.4 KB | Display | ![]() |
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PDB format | ![]() | 183.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.7 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 49.2 KB | Display | |
Data in CIF | ![]() | 71.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bmcC ![]() 3bmnC ![]() 3bmoC ![]() 3bmqC ![]() 3jq6C ![]() 3jq7C ![]() 3jq9C ![]() 3jqaC ![]() 3jqbC ![]() 3jqcC ![]() 3jqdC ![]() 3jqeC ![]() 3jqfC ![]() 3jqgC ![]() 2c7vS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Pteridine reductase ... , 2 types, 4 molecules ABCD
#1: Protein | Mass: 30669.791 Da / Num. of mol.: 1 / Fragment: UNP residues 102-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Protein | Mass: 30685.787 Da / Num. of mol.: 3 / Fragment: UNP residues 102-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 4 types, 985 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/DX3.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DX3.gif)
![](data/chem/img/DTT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-DX3 / #5: Chemical | ChemComp-DTT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 2-3M Sodium acetate, 10-100mM Sodium citrate, pH 4.0-6.0, VAPOR DIFFUSION, temperature 293K PH range: 4.0-6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2005 Details: Liquid nitrogen cooled channel-cut silicon monochromator and a cylindrical grazing incidence mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: high resolution Si(311) cut and a lower resolution Si(111) cut Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9755 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.95→66.89 Å / Num. obs: 70867 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 10.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2C7V Resolution: 1.95→66.89 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.833 / WRfactor Rfree: 0.272 / WRfactor Rwork: 0.225 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.666 / SU B: 8.444 / SU ML: 0.226 / SU R Cruickshank DPI: 0.242 / SU Rfree: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.203 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 291.6 Å2 / Biso mean: 15.454 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→66.89 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1695 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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