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- PDB-6pf4: Crystal structure of human thymidylate synthase Delta (7-29) in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6pf4 | |||||||||
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Title | Crystal structure of human thymidylate synthase Delta (7-29) in complex with dUMP and 2-(2-(4-((2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)methyl)benzamido)phenyl)acetic acid | |||||||||
![]() | Thymidylate synthase | |||||||||
![]() | transferase/transferase inhibitor / inhibitor / TS / TRANSFERASE / transferase-transferase inhibitor complex | |||||||||
Function / homology | ![]() uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion ...uracil metabolic process / response to organophosphorus / intestinal epithelial cell maturation / response to folic acid / Interconversion of nucleotide di- and triphosphates / thymidylate synthase / response to vitamin A / sequence-specific mRNA binding / cartilage development / tetrahydrofolate interconversion / thymidylate synthase activity / folic acid binding / dTMP biosynthetic process / dTTP biosynthetic process / DNA biosynthetic process / G1/S-Specific Transcription / developmental growth / dihydrofolate reductase activity / response to glucocorticoid / mRNA regulatory element binding translation repressor activity / response to cytokine / response to progesterone / liver regeneration / response to toxic substance / circadian rhythm / methylation / response to ethanol / mitochondrial inner membrane / negative regulation of translation / mitochondrial matrix / response to xenobiotic stimulus / protein homodimerization activity / mitochondrion / nucleus / cytoplasm / 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 | ![]() | 232.9 KB | Display | ![]() |
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PDB format | ![]() | 185 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 697 KB | Display | ![]() |
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Full document | ![]() | 700.7 KB | Display | |
Data in XML | ![]() | 2.5 KB | Display | |
Data in CIF | ![]() | 13.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6pf3C ![]() 6pf5C ![]() 6pf6C ![]() 6pf7C ![]() 6pf8C ![]() 6pf9C ![]() 6pfaC ![]() 6pfbC ![]() 6pfcC ![]() 6pfdC ![]() 6pfeC ![]() 6pffC ![]() 6pfgC ![]() 6pfhC ![]() 6pfiC ![]() 1hzwS 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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Unit cell |
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Components
#1: Protein | Mass: 33189.070 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-UMP / #3: Chemical | ChemComp-OF7 / [ #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.8 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Well solution 28 % PEG 4000, 0.2 M lithium sulfate, 0.1 M Tris Drop ratio 1:1 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: Feb 9, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 28415 / % possible obs: 97.6 % / Redundancy: 7 % / CC1/2: 0.995 / Rsym value: 0.176 / Net I/σ(I): 10.29 |
Reflection shell | Resolution: 2.84→3.02 Å / Redundancy: 6 % / Mean I/σ(I) obs: 3.2 / Num. unique obs: 3981 / CC1/2: 0.928 / Rsym value: 0.737 / % possible all: 86 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1HZW Resolution: 2.854→47.547 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.854→47.547 Å
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Refine LS restraints |
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LS refinement shell |
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