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- PDB-7opj: Trypanosoma brucei PTR1 (TbPTR1) in complex with pyrimethamine -

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Basic information

Entry
Database: PDB / ID: 7opj
TitleTrypanosoma brucei PTR1 (TbPTR1) in complex with pyrimethamine
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / PTR1 / TbPTR1 / pyrimethamine
Function / homology
Function and homology information


pteridine reductase activity / nucleotide binding
Similarity search - Function
Pteridine reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-CP6 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsTassone, G. / Landi, G. / Pozzi, C. / Mangani, S.
CitationJournal: Pharmaceuticals / Year: 2021
Title: Evidence of Pyrimethamine and Cycloguanil Analogues as Dual Inhibitors of Trypanosoma brucei Pteridine Reductase and Dihydrofolate Reductase.
Authors: Tassone, G. / Landi, G. / Linciano, P. / Francesconi, V. / Tonelli, M. / Tagliazucchi, L. / Costi, M.P. / Mangani, S. / Pozzi, C.
History
DepositionMay 31, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pteridine reductase
B: Pteridine reductase
C: Pteridine reductase
D: Pteridine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,97617
Polymers122,6794
Non-polymers4,29713
Water18,4291023
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23530 Å2
ΔGint-161 kcal/mol
Surface area30970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.900, 91.030, 82.800
Angle α, β, γ (deg.)90.000, 115.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Pteridine reductase


Mass: 30669.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290

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Non-polymers , 5 types, 1036 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-CP6 / 5-(4-CHLORO-PHENYL)-6-ETHYL-PYRIMIDINE-2,4-DIAMINE / PYRIMETHAMINE


Mass: 248.711 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H13ClN4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1023 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 41.41 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2-2.5M sodium acetate, 0.1M sodium citrate, pH 5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 29, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.34→18.28 Å / Num. obs: 210248 / % possible obs: 93.9 % / Redundancy: 2.3 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.042 / Rrim(I) all: 0.071 / Net I/σ(I): 7.6
Reflection shellResolution: 1.34→1.41 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 30679 / CC1/2: 0.883 / Rpim(I) all: 0.27 / Rrim(I) all: 0.44 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TBX

6tbx


Resolution: 1.34→18.07 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.992 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1739 10516 5 %RANDOM
Rwork0.1301 ---
obs0.1323 199465 93.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.21 Å2 / Biso mean: 18.906 Å2 / Biso min: 6.78 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.08 Å2
2---0.45 Å2-0 Å2
3---0.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.1492 Å
Refinement stepCycle: final / Resolution: 1.34→18.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7289 0 282 1025 8596
Biso mean--17.84 34.79 -
Num. residues----990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0128006
X-RAY DIFFRACTIONr_angle_refined_deg2.0761.67311034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21851100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73122.5336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.715151248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9031544
X-RAY DIFFRACTIONr_chiral_restr0.120.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.026028
X-RAY DIFFRACTIONr_rigid_bond_restr5.04237435
LS refinement shellResolution: 1.34→1.375 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 790 -
Rwork0.231 14665 -
all-15455 -
obs--93.76 %

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