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- PDB-3jqa: 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: 3jqa | |||||||||
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Title | Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and inhibitor 2-amino-1,9-dihydro-6H-purine-6-thione (DX4) | |||||||||
![]() | (Pteridine reductase ...) x 3 | |||||||||
![]() | 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 | ![]() | 221.4 KB | Display | ![]() |
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PDB format | ![]() | 175 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 | ![]() | 44.5 KB | Display | |
Data in CIF | ![]() | 63.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bmcC ![]() 3bmnC ![]() 3bmoC ![]() 3bmqC ![]() 3jq6C ![]() 3jq7C ![]() 3jq8C ![]() 3jq9C ![]() 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 ... , 3 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.: 2 / Fragment: UNP residues 102-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | | Mass: 30701.787 Da / Num. of mol.: 1 / Fragment: UNP residues 102-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Non-polymers , 3 types, 646 molecules ![](data/chem/img/NAP.gif)
![](data/chem/img/DX4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DX4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-DX4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.58 % |
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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: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 21, 2006 Details: Pt coated mirrors in a Kirkpatrick-Baez (KB) geometry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→57.64 Å / Num. obs: 78741 / % possible obs: 99.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2C7V Resolution: 1.9→57.64 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.157 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.902 / SU B: 5.582 / SU ML: 0.083 / SU R Cruickshank DPI: 0.128 / SU Rfree: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.123 / 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: 88.34 Å2 / Biso mean: 23.802 Å2 / Biso min: 6.32 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→57.64 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 2957 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.9→1.949 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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