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- PDB-1of1: KINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1... -

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Basic information

Entry
Database: PDB / ID: 1of1
TitleKINETICS AND CRYSTAL STRUCTURE OF THE HERPES SIMPLEX VIRUS TYPE 1 THYMIDINE KINASE INTERACTING WITH (SOUTH)-METHANOCARBA-THYMIDINE
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / THYMIDINE KINASE / ANTIVIRAL DRUG / ENZYME-PRODRUG GENE / KINASE / DNA SYNTHESIS / ATP-BINDING
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
(SOUTH)-METHANOCARBA-THYMIDINE / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHERPES SIMPLEX VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsClaus, M.T. / Schelling, P. / Folkers, G. / Marquez, V.E. / Scapozza, L. / Schulz, G.E.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Biochemical and Structural Characterization of (South)-Methanocarbathymidine that Specifically Inhibits Growth of Herpes Simplex Virus Type 1 Thymidine Kinase-Transduced Osteosarcoma Cells
Authors: Schelling, P. / Claus, M.T. / Johner, R. / Marquez, V.E. / Schulz, G.E. / 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.
History
DepositionApr 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDINE KINASE
B: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7326
Polymers82,0362
Non-polymers6974
Water6,125340
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.730, 118.010, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.92536, -0.32539, -0.19448), (-0.3241, 0.41298, 0.85112), (-0.19663, 0.85063, -0.48761)
Vector: 74.97475, 23.2395, -9.95733)

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Components

#1: Protein THYMIDINE KINASE


Mass: 41017.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
Strain: 17 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SCT / (SOUTH)-METHANOCARBA-THYMIDINE


Mass: 252.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H16N2O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8453
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 52523 / % possible obs: 99.2 % / Redundancy: 5.2 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.166 / % possible all: 99

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2K

1e2k


Resolution: 1.95→40 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3292353.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2649 5 %RANDOM
Rwork0.184 ---
obs0.184 52523 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.1761 Å2 / ksol: 0.358386 e/Å3
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--4.29 Å2--
2--10.97 Å2-
3----6.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-40 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.95→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4737 0 46 340 5123
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.851.5
X-RAY DIFFRACTIONc_mcangle_it3.812
X-RAY DIFFRACTIONc_scbond_it4.212
X-RAY DIFFRACTIONc_scangle_it5.542.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 445 5.3 %
Rwork0.198 7877 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4SMC.PARSMC.TOP

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