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- PDB-2j87: Structure of vaccinia virus thymidine kinase in complex with dTTP... -

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Basic information

Entry
Database: PDB / ID: 2j87
TitleStructure of vaccinia virus thymidine kinase in complex with dTTP: insights for drug design
ComponentsTHYMIDINE KINASE
KeywordsTRANSFERASE / TYPE 2 THYMIDINE KINASE / DNA SYNTHESIS / NUCLEOTIDE-BINDING / DTTP / KINASE / ATP-BINDING / VACCINIA VIRUS THYMIDINE KINASE
Function / homology
Function and homology information


thymidine kinase / thymidine kinase activity / DNA biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Thymidine kinase
Similarity search - Component
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsEl Omari, K. / Solaroli, N. / Karlsson, A. / Balzarini, J. / Stammers, D.K.
CitationJournal: Bmc Struct.Biol. / Year: 2006
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
DepositionOct 23, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: THYMIDINE KINASE
B: THYMIDINE KINASE
C: THYMIDINE KINASE
D: THYMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,55216
Polymers80,2654
Non-polymers2,28812
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)63.331, 63.331, 166.412
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYTYRTYRAA4 - 404 - 40
21GLYGLYTYRTYRBB4 - 404 - 40
31GLYGLYTYRTYRCC4 - 404 - 40
41GLYGLYTYRTYRDD4 - 404 - 40
12ALAALAVALVALAA60 - 17560 - 175
22ALAALAVALVALBB60 - 17560 - 175
32ALAALAVALVALCC60 - 17560 - 175
42ALAALAVALVALDD60 - 17560 - 175

NCS ensembles :
ID
1
2

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Components

#1: Protein
THYMIDINE KINASE / / VACCINIA VIRUS THYMIDINE KINASE


Mass: 20066.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O57203, thymidine kinase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growpH: 6.5
Details: 2-7% POLYETHYLENE GLYCOL 3350, 5MM MGSO4 AND 50MM MES PH6.5, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W4R

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.
RfactorNum. reflection% reflectionSelection details
Rfree0.289 637 5 %RANDOM
Rwork0.257 ---
obs0.258 12144 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.97 Å2
Baniso -1Baniso -2Baniso -3
1-3.69 Å21.84 Å20 Å2
2--3.69 Å20 Å2
3----5.53 Å2
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5206 0 124 0 5330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225398
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9917271
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.43624.527243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.464151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4371533
X-RAY DIFFRACTIONr_chiral_restr0.0850.2818
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023908
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.270.23032
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23806
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2242
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4830.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.191.53314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.32725247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.48532306
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.8274.52024
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A306tight positional0.040.05
12B306tight positional0.040.05
13C306tight positional0.040.05
14D306tight positional0.040.05
21A905tight positional0.040.05
22B905tight positional0.040.05
23C905tight positional0.040.05
24D905tight positional0.040.05
11A306tight thermal0.060.5
12B306tight thermal0.050.5
13C306tight thermal0.060.5
14D306tight thermal0.060.5
21A905tight thermal0.050.5
22B905tight thermal0.050.5
23C905tight thermal0.050.5
24D905tight thermal0.050.5
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.393 58
Rwork0.386 882
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.44512.0157-0.67963.4805-0.82744.24350.00420.3017-0.4459-0.31640.0387-0.14790.7155-0.0512-0.0430.0780.09440.0453-0.1099-0.0322-0.185-3.125-7.752-12.042
24.76441.6077-0.73682.6311-0.191.93790.1359-0.37670.15390.4489-0.05560.2431-0.3442-0.2031-0.08030.05750.062-0.0114-0.0368-0.0424-0.1997-17.29216.30311.83
34.75862.13270.42652.8327-0.64253.5583-0.03250.39170.1117-0.38880.01320.1874-0.2924-0.53160.0193-0.04270.1184-0.01270.0613-0.0805-0.1672-21.06613.166-13.211
43.40231.08150.01482.2025-0.31384.53970.0568-0.2276-0.20430.1871-0.1288-0.2940.21540.17070.072-0.11410.0536-0.0258-0.12270.013-0.1431-2.794-6.10713.506
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 175
2X-RAY DIFFRACTION2B4 - 175
3X-RAY DIFFRACTION3C4 - 175
4X-RAY DIFFRACTION4D4 - 175

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