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- PDB-1of1: KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1of1 | ||||||
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Title | KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE | ||||||
![]() | THYMIDINE KINASE | ||||||
![]() | TRANSFERASE / THYMIDINE KINASE / ANTIVIRAL DRUG / ENZYME-PRODRUG GENE / KINASE / DNA SYNTHESIS / ATP-BINDING | ||||||
Function / homology | ![]() TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Claus, M.T. / Schelling, P. / Folkers, G. / Marquez, V.E. / Scapozza, L. / Schulz, G.E. | ||||||
![]() | ![]() Title: Biochemical and Structural Characterization of (South)-Methanocarbathymidine that Specifically Inhibits Growth of Herpes Simplex Virus Type 1 Thymidine Kinase-Transduced Osteosarcoma Cells Authors: Schelling, P. / Claus, M.T. / Johner, R. / Marquez, V.E. / Schulz, G.E. / Scapozza, L. #1: Journal: FEBS Lett. / Year: 1995 Title: The Three-Dimensional Structure of Thymidine Kinase from Herpes Simplex Virus Type 1 Authors: Wild, K. / Bohner, T. / Aubry, A. / Folkers, G. / Schulz, G.E. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 138.1 KB | Display | ![]() |
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PDB format | ![]() | 107.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 28 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1e2kS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92536, -0.32539, -0.19448), Vector: |
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Components
#1: Protein | Mass: 41017.875 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 17 / Production host: ![]() ![]() References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.41 % |
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Crystal grow | pH: 7.5 / Details: pH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8453 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→40 Å / Num. obs: 52523 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.049 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.166 / % possible all: 99 |
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Processing
Software | Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1E2K Resolution: 1.95→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3292353.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.1761 Å2 / ksol: 0.358386 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Xplor file |
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