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- PDB-1e2k: Kinetics and crystal structure of the wild-type and the engineere... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e2k | ||||||
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Title | Kinetics and crystal structure of the wild-type and the engineered Y101F mutant of Herpes simplex virus type 1 thymidine kinase interacting with (North)-methanocarba-thymidine | ||||||
![]() | THYMIDINE KINASE | ||||||
![]() | TRANSFERASE / THYMIDINE KINASE / ANTIVIRAL DRUG / ENZYME-PRODRUG GENE THERAPY / SUGAR RING PUCKER | ||||||
Function / homology | ![]() TMP biosynthetic process / thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vogt, J. / Scapozza, L. / Schulz, G.E. | ||||||
![]() | ![]() Title: Kinetics and Crystal Structure of the Wild-Type and the Engineered Y101F Mutant of Herpes Simplex Virus Type 1 Thymidine Kinase Interacting with (North)-Methanocarba-Thymidine Authors: Prota, A. / Vogt, J. / Pilger, B. / Perozzo, R. / Wurth, C. / Marquez, V. / Russ, P. / Schulz, G.E. / Folkers, G. / 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. #2: Journal: Nat.Struct.Biol. / Year: 1995 Title: Crystal Structures of the Thymidine Kinase from Herpes Simplex Virus Type-1 in Complex with Deoxythymidine and Ganciclovir Authors: Brown, D.G. / Visse, R. / Sandhu, G. / Davies, A. / Rizkallah, P.J. / Melitz, C. / Summers, W.C. / Sanderson, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 139 KB | Display | ![]() |
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PDB format | ![]() | 108.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1e2lC ![]() 1vtkS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.92536, -0.3241, -0.19663), Vector: Details | THE STRONG CRYSTAL PACKING GENERATED USING X , 1-Y, -Z GIVESCHAIN A TO CHAIN A (SYMMETRY RELATED) CONTACTS. | |
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Components
#1: Protein | Mass: 35779.086 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() 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: 2.54 Å3/Da / Density % sol: 51.5 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: LITHIUM SULFATE, HEPES, DTT, pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / pH: 8 / Method: vapor diffusion, sitting 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: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 12, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8468 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 79549 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.58 / % possible all: 99 |
Reflection | *PLUS % possible obs: 99 % / Rmerge(I) obs: 0.05 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1VTK Resolution: 1.7→20 Å / SU B: 1.3 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.11
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Displacement parameters | Biso mean: 32.7 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.209 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |