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Yorodumi- PDB-2vtk: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2vtk | |||||||||
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Title | THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND DEOXYTHYMIDINE | |||||||||
Components | THYMIDINE KINASE | |||||||||
Keywords | TRANSFERASE / KEY ENZYME IN THYMIDINE SALVAGE PATHWAY / ADDITIONAL THYMIDYLATE KINASE ACTIVITY / TARGET FOR ANTI-HERPES VIRAL DRUGS | |||||||||
Function / homology | Function and homology information TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / phosphorylation / ATP binding Similarity search - Function | |||||||||
Biological species | Herpes simplex virus | |||||||||
Method | X-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.8 Å | |||||||||
Authors | Wild, K. / Schulz, G.E. | |||||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue. Authors: Wild, K. / Bohner, T. / Folkers, G. / Schulz, G.E. #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. #2: Journal: Protein Expr.Purif. / Year: 1994 Title: A Fast Method for Obtaining Highly Pure Recombinant Herpes Simplex Virus Type 1 Thymidine Kinase Authors: Fetzer, J. / Michael, M. / Bohner, T. / Hofbauer, R. / Folkers, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2vtk.cif.gz | 75.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2vtk.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 2vtk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vtk_validation.pdf.gz | 762.6 KB | Display | wwPDB validaton report |
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Full document | 2vtk_full_validation.pdf.gz | 766.8 KB | Display | |
Data in XML | 2vtk_validation.xml.gz | 13.8 KB | Display | |
Data in CIF | 2vtk_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vt/2vtk ftp://data.pdbj.org/pub/pdb/validation_reports/vt/2vtk | HTTPS FTP |
-Related structure data
-Links
-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: 37205.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Herpes simplex virus (type 1 / strain F) Genus: Simplexvirus / Species: Human herpesvirus 1 / Strain: F / Plasmid: PGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): KY 895 References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-THM / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.65 Å3/Da / Density % sol: 67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Wild, K., (1995) FEBS Lett., 368, 289. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1996 |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→100 Å / Num. obs: 11472 / % possible obs: 83.1 % / Redundancy: 2.3 % / Biso Wilson estimate: 33 Å2 / Rsym value: 0.045 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.8→2.89 Å / Mean I/σ(I) obs: 3.4 / Rsym value: 0.189 / % possible all: 63.7 |
Reflection | *PLUS Num. measured all: 26826 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 63.7 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER / Resolution: 2.8→10 Å / Rfactor Rfree error: 0.007 / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 32.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.27 Å / Luzzati d res low obs: 4.8 Å / Luzzati sigma a obs: 0.46 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.92 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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