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- PDB-6pfd: 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: 6pfd | |||||||||
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Title | Crystal structure of TS-DHFR from Cryptosporidium hominis in complex with NADPH, FdUMP and 2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)terephthalic 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. / Valhondo, M. / Jorgensen, W.L. / Anderson, K.S. | |||||||||
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 | ![]() | 517.1 KB | Display | ![]() |
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PDB format | ![]() | 426 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6pf3C ![]() 6pf4C ![]() 6pf5C ![]() 6pf6C ![]() 6pf7C ![]() 6pf8C ![]() 6pf9C ![]() 6pfaC ![]() 6pfbC ![]() 6pfcC ![]() 6pfeC ![]() 6pffC ![]() 6pfgC ![]() 6pfhC ![]() 6pfiC ![]() 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
#1: Protein | Mass: 60262.520 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-UFP / #4: Chemical | ChemComp-OEJ / #5: Chemical | ChemComp-MTX / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.63 Å3/Da / Density % sol: 73.5 % |
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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 EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 3.32→50 Å / Num. obs: 75886 / % possible obs: 95.9 % / Redundancy: 3.7 % / CC1/2: 0.987 / Rsym value: 0.163 / Net I/σ(I): 9.04 |
Reflection shell | Resolution: 3.32→3.52 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.86 / Num. unique obs: 10354 / CC1/2: 0.816 / Rsym value: 0.714 / % possible all: 81.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4Q0E Resolution: 3.324→48.426 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.92
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.324→48.426 Å
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Refine LS restraints |
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LS refinement shell |
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