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- PDB-3tmk: CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3tmk | ||||||
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Title | CRYSTAL STRUCTURE OF YEAST THYMIDYLATE KINASE COMPLEXED WITH THE BISUBSTRATE INHIBITOR TP5A AT 2.0 A RESOLUTION: IMPLICATIONS FOR CATALYSIS AND AZT ACTIVATION | ||||||
![]() | THYMIDYLATE KINASE | ||||||
![]() | KINASE / PHOSPHOTRANSFERASE | ||||||
Function / homology | ![]() UMP/dUMP kinase activity / Interconversion of nucleotide di- and triphosphates / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion ...UMP/dUMP kinase activity / Interconversion of nucleotide di- and triphosphates / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lavie, A. / Schlichting, I. / Konrad, M. / Goody, R.S. / Brundiers, R. / Reinstein, J. | ||||||
![]() | ![]() Title: Crystal structure of yeast thymidylate kinase complexed with the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-thymidyl) pentaphosphate (TP5A) at 2.0 A resolution: implications for catalysis and AZT activation. Authors: Lavie, A. / Konrad, M. / Brundiers, R. / Goody, R.S. / Schlichting, I. / Reinstein, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 374.9 KB | Display | ![]() |
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PDB format | ![]() | 308.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.3 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 84 KB | Display | |
Data in CIF | ![]() | 112.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tmkS 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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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 24719.375 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-T5A / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 51 % |
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Crystal grow | pH: 4.6 / Details: pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1996 |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.8 Å / Num. obs: 116451 / % possible obs: 82 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.059 |
Reflection | *PLUS Num. measured all: 270178 |
Reflection shell | *PLUS % possible obs: 56.9 % / Rmerge(I) obs: 0.266 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1TMK Resolution: 2→43.8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 20.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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