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- PDB-2j87: Structure of vaccinia virus thymidine kinase in complex with dTTP... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2j87 | ||||||
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Title | Structure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design | ||||||
![]() | THYMIDINE KINASE | ||||||
![]() | TRANSFERASE / TYPE 2 THYMIDINE KINASE / DNA SYNTHESIS / NUCLEOTIDE-BINDING / DTTP / KINASE / ATP-BINDING / VACCINIA VIRUS THYMIDINE KINASE | ||||||
Function / homology | ![]() thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | El Omari, K. / Solaroli, N. / Karlsson, A. / Balzarini, J. / Stammers, D.K. | ||||||
![]() | ![]() Title: Structure of Vaccinia Virus Thymidine Kinase in Complex with Dttp: Insights for Drug Design. Authors: El Omari, K. / Solaroli, N. / Karlsson, A. / Balzarini, J. / Stammers, D.K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.2 KB | Display | ![]() |
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PDB format | ![]() | 109.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 30.2 KB | Display | |
Data in CIF | ![]() | 38.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w4rS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 1
NCS ensembles :
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Components
#1: Protein | Mass: 20066.211 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-TTP / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.37 % |
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Crystal grow | pH: 6.5 Details: 2-7% POLYETHYLENE GLYCOL 3350, 5MM MGSO4 AND 50MM MES PH6.5, pH 6.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. obs: 13636 / % possible obs: 94.8 % / Observed criterion σ(I): 2.3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.3 / % possible all: 87.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1W4R Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.836 / SU B: 72.92 / SU ML: 0.572 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.615 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.97 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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