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- PDB-2ki5: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG A... -

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Basic information

Entry
Database: PDB / ID: 2ki5
TitleHERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION
ComponentsPROTEIN (THYMIDINE KINASE)
KeywordsTRANSFERASE / TRANSFERASE (PHOSPHOTRANSFERASE) THYMID / TRANSFERASE (PHOSPHOTRANSFERASE) THYMIDINE KINASE / VIRIDAE / DS-DNA ENVELOPED VIRUSES / HERPESVIRIDAE / ALPHAHERPESVIRINAE ANTIVIRAL DRUG (ACICLOVIR)
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
9-HYROXYETHOXYMETHYLGUANINE / Thymidine kinase / Thymidine kinase
Similarity search - Component
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBennett, M.S. / Wien, F. / Champness, J.N. / Batuwangala, T. / Rutherford, T. / Summers, W.C. / Sun, H. / Wright, G. / Sanderson, M.R.
CitationJournal: FEBS Lett. / Year: 1999
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
DepositionFeb 12, 1999Deposition site: BNL / Processing site: RCSB
SupersessionMar 2, 1999ID: 1KI5
Revision 1.0Mar 4, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (THYMIDINE KINASE)
B: PROTEIN (THYMIDINE KINASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3686
Polymers79,7252
Non-polymers6434
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-61 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.100, 117.800, 108.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (THYMIDINE KINASE) / TK


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.) Human herpesvirus 1 (Herpes simplex virus type 1)
Genus: Simplexvirus / Strain: SY211 / Gene: TK / Plasmid: PT7:HSVTK / Gene (production host): TK / Production host: Escherichia coli (E. coli) / Strain (production host): SY211
References: UniProt: P03176, UniProt: P0DTH5*PLUS, thymidine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AC2 / 9-HYROXYETHOXYMETHYLGUANINE


Mass: 225.205 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H11N5O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growpH: 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
IDConc.Common nameCrystal-IDSol-ID
11.0 mg/mlprotein1drop
240 mMTris-HCl1drop
33 mMdithiothreitol1drop
40.2 mMdeoxythymidine1drop
530 %satammonium sulfate1reservoir
6200 mMTris-HCl1reservoir
73 mMdithiothreitol1reservoir
80.2 mMdeoxythymidine1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS
RadiationMonochromator: OTWINOWSKI MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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
NameVersionClassification
X-PLORmodel building
X-PLOR3.1Frefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KIM

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.317 4766 10 %RANDOM
Rwork0.241 ---
obs-47727 83 %-
Displacement parametersBiso mean: 23.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 1.9→16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4627 0 47 292 4966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.85
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.31
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.474
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.53
X-RAY DIFFRACTIONx_mcangle_it24
X-RAY DIFFRACTIONx_scbond_it1.53
X-RAY DIFFRACTIONx_scangle_it24
Refine LS restraints NCSNCS model details: NCS RESTRAINT NOT USED IN FINAL REFT. STAGES.
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.38 323 10 %
Rwork0.334 3057 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1JNC_PARHCSDX.PROJNC_TOPH19.SOL
X-RAY DIFFRACTION2JNC_PARAM19.SOLJNC_TOPHCSDX.PRO
X-RAY DIFFRACTION3JNC_SO4.PAR ALSO JNC_GAN.JNC_SO4.TOP
X-RAY DIFFRACTION4JNC_PARNAH1E.DNAACIC.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / % reflection Rfree: 10 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.31
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.474
LS refinement shell
*PLUS
Highest resolution: 1.9 Å

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