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- PDB-3t60: 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase -

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Basic information

Entry
Database: PDB / ID: 3t60
Title5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase, putative
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Trimeric dUTPase / dUTP binding / Nucleus / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


tRNA metabolic process / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / DNA replication / magnesium ion binding / identical protein binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2',5'-dideoxy-5'-(tritylamino)uridine / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.396 Å
AuthorsHampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. ...Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H.
CitationJournal: Chemmedchem / Year: 2011
Title: Design, synthesis, and evaluation of 5'-diphenyl nucleoside analogues as inhibitors of the Plasmodium falciparum dUTPase.
Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / ...Authors: Hampton, S.E. / Baragana, B. / Schipani, A. / Bosch-Navarrete, C. / Musso-Buendia, J.A. / Recio, E. / Kaiser, M. / Whittingham, J.L. / Roberts, S.M. / Shevtsov, M. / Brannigan, J.A. / Kahnberg, P. / Brun, R. / Wilson, K.S. / Gonzalez-Pacanowska, D. / Johansson, N.G. / Gilbert, I.H.
History
DepositionJul 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7089
Polymers62,0233
Non-polymers1,6856
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-37 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.972, 76.972, 106.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative


Mass: 20674.328 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF11_0282 / Plasmid: pET-20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8II92, dUTP diphosphatase
#2: Chemical ChemComp-DUA / 2',5'-dideoxy-5'-(tritylamino)uridine


Mass: 469.532 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H27N3O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.2M ammonium sulphate, 0.1M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 13, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.396→40 Å / Num. all: 24538 / Num. obs: 24538 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.3.0037refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYQ

1vyq


Resolution: 2.396→40 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.805 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2536 1244 5.1 %RANDOM
Rwork0.19618 ---
all0.19905 24538 --
obs0.19905 23083 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.671 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---0.55 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.396→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 123 96 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0223247
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.5082.0284388
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5925399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.79724.454119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.29715525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9251511
X-RAY DIFFRACTIONr_chiral_restr0.430.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022365
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.21252
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.22163
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2340.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.52054
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.01223189
X-RAY DIFFRACTIONr_scbond_it3.06931368
X-RAY DIFFRACTIONr_scangle_it4.4924.51199
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.396→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 79 -
Rwork0.247 1598 -
obs--93.63 %

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