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- PDB-6pfi: Crystal structure of TS-DHFR from Cryptosporidium hominis in comp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pfi | |||||||||
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Title | Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP and 3-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)-4-(carboxymethyl)benzoic acid. | |||||||||
![]() | Bifunctional dihydrofolate reductase-thymidylate synthase | |||||||||
![]() | transferase/transferase inhibitor / Inhibitor / TS / TS-DHFR / TRANSFERASE / transferase-transferase inhibitor complex | |||||||||
Function / homology | ![]() thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding / mitochondrion / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Czyzyk, D.J. / Anderson, K.S. / Jorgensen, W.L. / Valhondo, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure activity relationship towards design of cryptosporidium specific thymidylate synthase inhibitors. Authors: Czyzyk, D.J. / Valhondo, M. / Deiana, L. / Tirado-Rives, J. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 523 KB | Display | ![]() |
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PDB format | ![]() | 427.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 5.6 MB | Display | ![]() |
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Full document | ![]() | 5.7 MB | Display | |
Data in XML | ![]() | 93.2 KB | Display | |
Data in CIF | ![]() | 117 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pf3C ![]() 6pf4C ![]() 6pf5C ![]() 6pf6C ![]() 6pf7C ![]() 6pf8C ![]() 6pf9C ![]() 6pfaC ![]() 6pfbC ![]() 6pfcC ![]() 6pfdC ![]() 6pfeC ![]() 6pffC ![]() 6pfgC ![]() 6pfhC ![]() 4q0eS 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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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 60262.520 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 46 molecules ![](data/chem/img/NDP.gif)
![](data/chem/img/UFP.gif)
![](data/chem/img/OEP.gif)
![](data/chem/img/MTX.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/UFP.gif)
![](data/chem/img/OEP.gif)
![](data/chem/img/MTX.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-UFP / #4: Chemical | ChemComp-OEP / #5: Chemical | ChemComp-MTX / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.69 Å3/Da / Density % sol: 73.8 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Well solution 18% PEG 6000, 0.2 M ammonium sulfate, 0.06 M lithium sulfate, 0.1 M Tris Drop ratio 2:1 enzyme mix/well solution |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.89→50 Å / Num. obs: 119315 / % possible obs: 98.2 % / Redundancy: 6.9 % / CC1/2: 0.985 / Rsym value: 0.255 / Net I/σ(I): 5.18 |
Reflection shell | Resolution: 2.89→3.06 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.16 / Num. unique obs: 18527 / CC1/2: 0.671 / Rsym value: 1.324 / % possible all: 95.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q0E Resolution: 2.89→48.589 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.87 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.89→48.589 Å
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Refine LS restraints |
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LS refinement shell |
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