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- PDB-2yoh: Plasmodium falciparum thymidylate kinase in complex with a urea-a... -

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Basic information

Entry
Database: PDB / ID: 2yoh
TitlePlasmodium falciparum thymidylate kinase in complex with a urea-alpha- deoxythymidine inhibitor
ComponentsTHYMIDYLATE KINASE
KeywordsTRANSFERASE / MALARIA / INHIBITOR
Function / homology
Function and homology information


dGMP kinase activity / Interconversion of nucleotide di- and triphosphates / guanylate kinase / GMP kinase activity / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / GMP biosynthetic process / dTTP biosynthetic process ...dGMP kinase activity / Interconversion of nucleotide di- and triphosphates / guanylate kinase / GMP kinase activity / dTMP kinase / dUDP biosynthetic process / dTDP biosynthetic process / dTMP kinase activity / GMP biosynthetic process / dTTP biosynthetic process / nucleoside diphosphate kinase activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Thymidylate kinase, conserved site / Thymidylate kinase signature. / Thymidylate kinase / Thymidylate kinase-like domain / Thymidylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-WMJ / Thymidylate kinase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,2614
Polymers49,4502
Non-polymers8112
Water7,909439
1
A: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1302
Polymers24,7251
Non-polymers4051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: THYMIDYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1302
Polymers24,7251
Non-polymers4051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.260, 58.430, 71.830
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein THYMIDYLATE KINASE


Mass: 24725.102 Da / Num. of mol.: 2
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-WMJ / 1-[[(2R,3S,5S)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl]-3-(4-nitrophenyl)urea


Mass: 405.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19N5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1 M BIS-TRIS PH 6.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→25.1 Å / Num. obs: 53617 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.7 / % 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: 1.6→71.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.382 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21921 2720 5.1 %RANDOM
Rwork0.16231 ---
obs0.16514 50880 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.169 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å2-0.86 Å2
2---0.46 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.6→71.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 58 439 3808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223642
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.431.9774959
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4135442
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38125.311177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43615676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2251510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212772
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_it1.4771.52069
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.27923391
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2431573
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.7154.51547
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.07433642
X-RAY DIFFRACTIONr_sphericity_free7.3263439
X-RAY DIFFRACTIONr_sphericity_bonded4.74733532
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 201 -
Rwork0.302 3741 -
obs--99.92 %

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