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- PDB-2ki5: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ki5 | |||||||||
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Title | HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION | |||||||||
![]() | PROTEIN (THYMIDINE KINASE) | |||||||||
![]() | ![]() ![]() ![]() | |||||||||
Function / homology | ![]() TMP biosynthetic process / ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bennett, M.S. / Wien, F. / Champness, J.N. / Batuwangala, T. / Rutherford, T. / Summers, W.C. / Sun, H. / Wright, G. / Sanderson, M.R. | |||||||||
![]() | ![]() Title: Structure to 1.9 A resolution of a complex with herpes simplex virus type-1 thymidine kinase of a novel, non-substrate inhibitor: X-ray crystallographic comparison with binding of aciclovir. Authors: Bennett, M.S. / Wien, F. / Champness, J.N. / Batuwangala, T. / Rutherford, T. / Summers, W.C. / Sun, H. / Wright, G. / 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 | ![]() | 136.2 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1qhiC ![]() 1kimS 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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Unit cell |
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Components
#1: Protein | Mass: 39862.570 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: ACICLOVIR, ANTIVIRAL DRUG AS DEPOSITED IN 1KI5 Source: (gene. exp.) ![]() ![]() ![]() Genus: Simplexvirus ![]() ![]() ![]() ![]() References: UniProt: P03176, UniProt: P0DTH5*PLUS, ![]() #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: 2.23 Å3/Da / Density % sol: 44.8 % | |||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow![]() | pH: 7.5 Details: CRYSTALLIZATION CONDITIONS: PUBLISHED IN BENNETT, M.S. ET AL. FEBS LETT., VOL.443 (1999) 121-125, pH 7.5 | |||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS |
Radiation | Monochromator: OTWINOWSKI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.82→16 Å / Num. obs: 63458 / % possible obs: 97 % / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Biso Wilson estimate: 23.7 Å2 / Rsym value: 0.045 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.82→1.87 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.25 / % possible all: 57 |
Reflection | *PLUS Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS % possible obs: 57 % |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: 1KIM Resolution: 1.9→16 Å / Isotropic thermal model: INDIVIDUAL B-FACTOR REFINEMENT / Cross valid method: FREE R / σ(F): 3 / Details: NCS RESTRAINTS NOT USED IN FINAL CYCLES.
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Displacement parameters | Biso mean: 23.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→16 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NCS RESTRAINT NOT USED IN FINAL REFT. STAGES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.97 Å / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor obs: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.9 Å |