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- PDB-1vyq: Novel inhibitors of Plasmodium Falciparum dUTPase provide a platf... -

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Basic information

Entry
Database: PDB / ID: 1vyq
TitleNovel inhibitors of Plasmodium Falciparum dUTPase provide a platform for anti-malarial drug design
ComponentsDEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
KeywordsHYDROLASE / DRUG DESIGN / PLASMODIUM FALCIPARUM / DUTPASE / DEOXYURIDINE NUCLEOTIDOHYDROLASE / MALARIA
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
2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesPLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsWhittingham, J.L. / Leal, I. / Kasinathan, G. / Nguyen, C. / Bell, E. / Jones, A.F. / Berry, C. / Benito, A. / Turkenburg, J.P. / Dodson, E.J. ...Whittingham, J.L. / Leal, I. / Kasinathan, G. / Nguyen, C. / Bell, E. / Jones, A.F. / Berry, C. / Benito, A. / Turkenburg, J.P. / Dodson, E.J. / Ruiz Perez, L.M. / Wilkinson, A.J. / Johansson, N.G. / Brun, R. / Gilbert, I.H. / Gonzalez Pacanowska, D. / Wilson, K.S.
CitationJournal: Structure / Year: 2005
Title: Dutpase as a Platform for Antimalarial Drug Design: Structural Basis for the Selectivity of a Class of Nucleoside Inhibitors.
Authors: Whittingham, J.L. / Leal, I. / Nguyen, C. / Kasinathan, G. / Bell, E. / Jones, A.F. / Berry, C. / Benito, A. / Turkenburg, J.P. / Dodson, E.J. / Ruiz Perez, L.M. / Wilkinson, A.J. / ...Authors: Whittingham, J.L. / Leal, I. / Nguyen, C. / Kasinathan, G. / Bell, E. / Jones, A.F. / Berry, C. / Benito, A. / Turkenburg, J.P. / Dodson, E.J. / Ruiz Perez, L.M. / Wilkinson, A.J. / Johansson, N.G. / Brun, R. / Gilbert, I.H. / Gonzalez Pacanowska, D. / Wilson, K.S.
History
DepositionMay 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
B: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
C: DEOXYURIDINE 5'-TRIPHOSPHATE NUCLEOTIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2276
Polymers58,8103
Non-polymers1,4183
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.830, 62.830, 121.527
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 / DUTP PYROPHOSPHATASE


Mass: 19603.174 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: INHIBITOR COMPLEX
Source: (gene. exp.) PLASMODIUM FALCIPARUM (malaria parasite P. falciparum)
Strain: 3D7 / Plasmid: PET11PFDUT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8II92, dUTP diphosphatase
#2: Chemical ChemComp-DUX / 2,3-DEOXY-3-FLUORO-5-O-TRITYLURIDINE / 1-{(2S,5S)-4-FLUORO-5-[(TRITYLOXY)METHYL]TETRAHYDROFURAN-2-YL}PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 472.508 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H25FN2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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 Å3/Da / Density % sol: 40 %
Crystal growpH: 7.1
Details: 10 MG/ML PROTEIN SOLUTION CONTAINING 3-FOLD EXCESS OF INHIBITOR. 0.1 M HEPES PH 7.1, 25% W/W PEG-MME 2000, 0.8 M SODIUM FORMATE

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 18324 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 1.4 / % possible all: 95

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MQ7

1mq7


Resolution: 2.4→40 Å / SU B: 10.347 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.431 / ESU R Free: 0.318
Details: ATOMS WITH ZERO OCCUPANCY WERE REMOVED DURING PDB DEPOSITION
RfactorNum. reflection% reflectionSelection details
Rfree0.295 934 5 %RANDOM
Rwork0.191 ---
obs0.196 18324 100 %-
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.28 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3103 0 105 119 3327

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