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- PDB-1uou: Crystal structure of human thymidine phosphorylase in complex wit... -
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Basic information
Entry | Database: PDB / ID: 1uou | ||||||
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Title | Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor | ||||||
![]() | THYMIDINE PHOSPHORYLASE | ||||||
![]() | TRANSFERASE / PHOSPHORYLASE / GLYCOSYLTRANSFERASE / CHEMOTAXIS / ANGIOGENESIS | ||||||
Function / homology | ![]() regulation of gastric motility / thymidine phosphorylase / dTMP catabolic process / pyrimidine nucleoside metabolic process / regulation of transmission of nerve impulse / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / Pyrimidine catabolism ...regulation of gastric motility / thymidine phosphorylase / dTMP catabolic process / pyrimidine nucleoside metabolic process / regulation of transmission of nerve impulse / pyrimidine-nucleoside phosphorylase activity / thymidine phosphorylase activity / pyrimidine nucleobase metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / Pyrimidine catabolism / Pyrimidine salvage / AMP catabolic process / mitochondrial genome maintenance / regulation of myelination / growth factor activity / chemotaxis / angiogenesis / cell differentiation / protein homodimerization activity / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / McAlister, M.S.B. / McCall, E.J. ...Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / McAlister, M.S.B. / McCall, E.J. / McMiken, H.H.J. / Paterson, D.S. / Timms, D. / Tucker, J.A. / Pauptit, R.A. | ||||||
![]() | ![]() Title: Crystal Structure of Human Thymidine Phosphorylase in Complex with a Small Molecule Inhibitor Authors: Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / Mcalister, M.S.B. / Mccall, E.J. / Mcmicken, H.H.J. / Paterson, D.S. / Timms, ...Authors: Norman, R.A. / Barry, S.T. / Bate, M. / Breed, J. / Colls, J.G. / Ernill, R.J. / Luke, R.W.A. / Minshull, C.A. / Mcalister, M.S.B. / Mccall, E.J. / Mcmicken, H.H.J. / Paterson, D.S. / Timms, D. / Tucker, J.A. / Pauptit, R.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 94.4 KB | Display | ![]() |
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PDB format | ![]() | 69.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.9 KB | Display | ![]() |
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Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 25.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1brwS 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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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 49195.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 12-408,411-482 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-CMU / |
#3: Water | ChemComp-HOH / |
Compound details | PYRIMIDINE NUCLEOSIDE METABOLISM, ALSO KNOWN AS PLATELET- DERIVED ENDOTHELIAL CELL GROWTH FACTOR ...PYRIMIDINE |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 8% PEG 1000(W/V), 50MM MALATE/IMIDAZOLE PH 6.5,100MM MGCL2. | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→91.3 Å / Num. obs: 15827 / % possible obs: 63.7 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 2.11→2.21 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.8 / % possible all: 11.2 |
Reflection | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 91.3 Å / Redundancy: 2.1 % / Num. measured all: 32998 / Rmerge(I) obs: 0.03 |
Reflection shell | *PLUS % possible obs: 11.2 % / Redundancy: 1.3 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 1.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BRW, CHAIN B Resolution: 2.11→91.29 Å / SU B: 9.266 / SU ML: 0.219 / Cross valid method: THROUGHOUT / ESU R: 0.63 / ESU R Free: 0.301 Details: RESIDUES 409-410 WERE REMOVED BY PROTEOLYSIS.RESIDUES 12-32, 238-239, 407-414 AND 481-482 WERE DISORDERED.
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Displacement parameters | Biso mean: 22.984 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→91.29 Å
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Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 91.3 Å | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.577 / Rfactor Rwork: 0.348 |