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- PDB-2yof: Plasmodium falciparum thymidylate kinase in complex with a (thio)... -

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Basic information

Entry
Database: PDB / ID: 2yof
TitlePlasmodium falciparum thymidylate kinase in complex with a (thio)urea- beta-deoxythymidine inhibitor
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / MALARIA
Function / homology
Function and homology information


T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity ...T2-induced deoxynucleotide kinase activity / guanylate kinase / Interconversion of nucleotide di- and triphosphates / guanylate kinase activity / dUDP biosynthetic process / dTMP kinase / thymidylate kinase activity / dTDP biosynthetic process / GMP biosynthetic process / nucleoside diphosphate kinase activity / dTTP biosynthetic process / phosphorylation / mitochondrion / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-74W / ACETATE ION / Thymidylate kinase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsHuaqing, C. / Carrero-Lerida, J. / Silva, A.P.G. / Whittingham, J.L. / Brannigan, J.A. / Ruiz-Perez, L.M. / Read, K.D. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Gilbert, I.H.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Synthesis and Evaluation of Alpha-Thymidine Analogues as Novel Antimalarials.
Authors: Cui, H. / Carrero-Lerida, J. / Silva, A.P.G. / Whittingham, J.L. / Brannigan, J.A. / Ruiz-Perez, L.M. / Read, K.D. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Gilbert, I.H.
History
DepositionOct 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THYMIDYLATE KINASE
B: THYMIDYLATE KINASE
C: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,23413
Polymers74,1753
Non-polymers2,05810
Water11,620645
1
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4264
Polymers24,7251
Non-polymers7013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4264
Polymers24,7251
Non-polymers7013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3815
Polymers24,7251
Non-polymers6564
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.639, 109.639, 121.892
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2163-

HOH

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Components

#1: Protein THYMIDYLATE KINASE


Mass: 24725.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8I4S1, dTMP kinase
#2: Chemical ChemComp-74W / 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-[[(2R,3S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]thiourea / (THIO)UREA-BETA-DEOXYTHYMIDINE DERIVATIVE


Mass: 478.873 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H18ClF3N4O4S
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7 / Details: 0.2 M TRI-AMMONIUM CITRATE PH 7.0, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.82→51.29 Å / Num. obs: 76207 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 12.9
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 10 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WWF

2wwf


Resolution: 1.82→94.95 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.984 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.23086 3825 5 %RANDOM
Rwork0.18856 ---
obs0.19067 72340 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20.87 Å20 Å2
2--1.73 Å20 Å2
3----2.6 Å2
Refinement stepCycle: LAST / Resolution: 1.82→94.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 135 645 5867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0225542
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4251.997530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2685646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48225.362276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.905151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2631517
X-RAY DIFFRACTIONr_chiral_restr0.0990.2791
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7481.53135
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37325102
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07532407
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3854.52407
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
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 272 -
Rwork0.304 5287 -
obs--100 %

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