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- PDB-3t6y: 5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase -

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Basic information

Entry
Database: PDB / ID: 3t6y
Title5'-Diphenyl Nucleoside Inhibitors of Plasmodium falciparum dUTPase
Components
  • Deoxyuridine 5'-triphosphate nucleotidohydrolase, putative
  • peptide ALA-HIS-ALA
KeywordsHYDROLASE/HYDROLASE INHIBITOR / 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
Chem-DU2 / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Source and taxonomy
Category: citation / pdbx_entity_src_syn
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.2Nov 1, 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
F: peptide ALA-HIS-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,86812
Polymers62,1954
Non-polymers1,6738
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-125 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.830, 76.830, 106.130
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: 20632.248 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: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8II92, dUTP diphosphatase
#2: Protein/peptide peptide ALA-HIS-ALA


Mass: 298.318 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-DU2 / 2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine


Mass: 397.428 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H23N5O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M Ammonium sulphate, 0.2M di-sodium phosphate, pH 7.0, 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: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.6→37.96 Å / Num. all: 19028 / Num. obs: 19028 / % possible obs: 100 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.012 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→37.96 Å / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0119refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VYQ

1vyq


Resolution: 2.6→37.96 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 8.548 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.435 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21761 958 5 %RANDOM
Rwork0.15115 ---
obs0.15441 18017 99.94 %-
all-19028 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.942 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.6→37.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 112 127 3713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023649
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0162.0214914
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3045431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24324.87154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.71515667
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5691514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212637
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 80 -
Rwork0.254 1272 -
obs--99.71 %

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