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- PDB-3vtk: THYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 3vtk
TitleTHYMIDINE KINASE FROM HERPES SIMPLEX VIRUS TYPE 1 IN COMPLEX WITH ADP AND 5-IODO-DEOXYURIDINE-MONOPHOSPHATE
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / 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 / ATP binding
Similarity search - Function
Herpesvirus thymidine kinase / Thymidine kinase from herpesvirus / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHerpes simplex virus
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 3 Å
AuthorsWild, 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
DepositionApr 1, 1997Processing site: BNL
Revision 1.0Oct 22, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0673
Polymers37,2061
Non-polymers8612
Water1086
1
A: THYMIDINE KINASE
hetero molecules

A: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1346
Polymers74,4112
Non-polymers1,7234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area6200 Å2
ΔGint-61 kcal/mol
Surface area22730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)83.700, 83.700, 156.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein THYMIDINE KINASE


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
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-5IU / 5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 434.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12IN2O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 67 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMMOPS1drop
20.5 mMEDTA1drop
31.5 mMdithiothreitol1drop
40.05 mMthymidine1drop
520 mg/mlprotain1drop
620-25 mMpotassium phosphate1drop
77.5-10 %PEG80001drop
80.01 %1dropNaN3
940-50 mMpotassium phosphate1reservoir
101 mMdithiothreitol1reservoir
110.05thymidine1reservoir
1215-20 %PEG80001reservoir
130.02 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→100 Å / Num. obs: 8723 / % possible obs: 77.1 % / Redundancy: 2.4 % / Rsym value: 0.084 / Net I/σ(I): 11
Reflection shellResolution: 3→3.16 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.244 / % possible all: 49.8
Reflection
*PLUS
Num. measured all: 21343 / Rmerge(I) obs: 0.084
Reflection shell
*PLUS
% possible obs: 49.8 % / Rmerge(I) obs: 0.244

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
MERGEdata scaling
X-PLORphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 3→10 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT
Details: ISOTROPIC THERMAL FACTORS WERE NOT REFINED AND CORRESPOND TO THE STRUCTURE WITH ADP AND DEOXYTHYMIDINE-MONOPHOSPHATE, PDB ENTRY 1VTK.
RfactorNum. reflection% reflectionSelection details
Rfree0.305 863 9.9 %RANDOM
Rwork0.222 ---
obs0.222 8411 78.8 %-
Refine analyzeLuzzati coordinate error obs: 0.32 Å / Luzzati d res low obs: 4.8 Å / Luzzati sigma a obs: 0.56 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 48 6 2445
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.94
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.13 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 65 11.2 %
Rwork0.289 579 -
obs--49.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOP19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.94
LS refinement shell
*PLUS
Rfactor Rfree: 0.42

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