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- PDB-5jdc: Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin) -

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Basic information

Entry
Database: PDB / ID: 5jdc
TitleTrypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin)
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / oxydoreductase / inhibitor
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
Chem-6JP / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsMangani, S. / Pozzi, C. / Di Pisa, F. / Landi, G. / Dello Iacono, L.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Commission603240 Italy
CitationJournal: J.Med.Chem. / Year: 2016
Title: Profiling of Flavonol Derivatives for the Development of Antitrypanosomatidic Drugs.
Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / ...Authors: Borsari, C. / Luciani, R. / Pozzi, C. / Poehner, I. / Henrich, S. / Trande, M. / Cordeiro-da-Silva, A. / Santarem, N. / Baptista, C. / Tait, A. / Di Pisa, F. / Dello Iacono, L. / Landi, G. / Gul, S. / Wolf, M. / Kuzikov, M. / Ellinger, B. / Reinshagen, J. / Witt, G. / Gribbon, P. / Kohler, M. / Keminer, O. / Behrens, B. / Costantino, L. / Tejera Nevado, P. / Bifeld, E. / Eick, J. / Clos, J. / Torrado, J. / Jimenez-Anton, M.D. / Corral, M.J. / Alunda, J.M. / Pellati, F. / Wade, R.C. / Ferrari, S. / Mangani, S. / Costi, M.P.
History
DepositionApr 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Jan 10, 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

Downloads & links

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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)127,18415
Polymers122,7914
Non-polymers4,39311
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint-134 kcal/mol
Surface area31220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.840, 90.040, 82.940
Angle α, β, γ (deg.)90.00, 115.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABDC

#1: Protein Pteridine reductase


Mass: 30685.787 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pet-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290
#2: Protein Pteridine reductase


Mass: 30733.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: pET-15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290

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Non-polymers , 5 types, 268 molecules

#3: 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
#4: Chemical
ChemComp-6JP / (2S)-5,7-dihydroxy-2-(3-hydroxy-4-methoxyphenyl)-2,3-dihydro-4H-1-benzopyran-4-one


Mass: 302.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H14O6
#5: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10mM DTT; Crystallization buffer: 0.1 M Sodium Citrate pH 5, 2.25 M Sodium Acetate
PH range: 5.0-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.78→53.68 Å / Num. obs: 92591 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 6.1
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.9 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X9G

2x9g


Resolution: 1.78→53.68 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.873 / Rfactor Rfree error: 0.13 / SU B: 3.475 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24057 4615 4.9 %RANDOM
Rwork0.20789 ---
obs0.20949 89348 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.656 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.78→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7263 0 294 257 7814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197760
X-RAY DIFFRACTIONr_bond_other_d0.0030.027427
X-RAY DIFFRACTIONr_angle_refined_deg1.9842.01210594
X-RAY DIFFRACTIONr_angle_other_deg1.0773.00216978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.635.03987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93324.097288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.925151186
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5031547
X-RAY DIFFRACTIONr_chiral_restr0.1090.21258
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218744
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021711
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_it1.8641.9423953
X-RAY DIFFRACTIONr_mcbond_other1.8621.9423952
X-RAY DIFFRACTIONr_mcangle_it2.7772.8914918
X-RAY DIFFRACTIONr_mcangle_other2.7772.8914919
X-RAY DIFFRACTIONr_scbond_it2.7092.4133807
X-RAY DIFFRACTIONr_scbond_other2.7062.4133807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1773.4765673
X-RAY DIFFRACTIONr_long_range_B_refined5.55717.1338741
X-RAY DIFFRACTIONr_long_range_B_other5.55717.1358742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 371 -
Rwork0.275 6587 -
obs--99.43 %

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