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- PDB-4cm3: 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: 4cm3 | ||||||
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Title | Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor | ||||||
![]() | PTERIDINE REDUCTASE 1 | ||||||
![]() | OXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Barrack, K.L. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structure-Based Design and Synthesis of Antiparasitic Pyrrolopyrimidines Targeting Pteridine Reductase 1. Authors: Khalaf, A.I. / Huggan, J.K. / Suckling, C.J. / Gibson, C.L. / Stewart, K. / Giordani, F. / Barrett, M.P. / Wong, P.E. / Barrack, K.L. / 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 | ![]() | 209.1 KB | Display | ![]() |
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PDB format | ![]() | 176 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4cl8C ![]() 4cldC ![]() 4cleC ![]() 4clhC ![]() 4cloC ![]() 4clrC ![]() 4clxC ![]() 4cm1C ![]() 4cm4C ![]() 4cm5C ![]() 4cm6C ![]() 4cm7C ![]() 4cm8C ![]() 4cm9C ![]() 4cmaC ![]() 4cmbC ![]() 4cmcC ![]() 4cmeC ![]() 4cmgC ![]() 4cmiC ![]() 4cmjC ![]() 4cmkC 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 30669.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 534 molecules ![](data/chem/img/DTU.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/KP2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NAP.gif)
![](data/chem/img/KP2.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-DTU / ( #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-KP2 / #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | DTU-CYSTEINE: DTU IS COVALENTLYSequence details | SEQUENCE CONTAINS ADDITIONAL | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39 % / Description: NONE |
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Crystal grow | Details: RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU SATURN 944 HG / Detector: CCD / Date: May 14, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→53.65 Å / Num. obs: 70625 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.95→1.99 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.6 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.95→53.71 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.764 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES WITH INSUFFICIENT ELECTRON DENSITY WERE NOT MODELED.
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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: 25.894 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→53.71 Å
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Refine LS restraints |
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