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- PDB-6gcp: Trypanosoma brucei PTR1 in complex with inhibitor 2d (F186) -

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Basic information

Entry
Database: PDB / ID: 6gcp
TitleTrypanosoma brucei PTR1 in complex with inhibitor 2d (F186)
ComponentsPteridine reductase
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / PTR1 / TbPTR1 / benzothiazole
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-EUK / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsPozzi, C. / Landi, G. / Mangani, S.
Funding support1items
OrganizationGrant numberCountry
European Commission603240
CitationJournal: J.Med.Chem. / Year: 2019
Title: Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections.
Authors: Linciano, P. / Pozzi, C. / Iacono, L.D. / di Pisa, F. / Landi, G. / Bonucci, A. / Gul, S. / Kuzikov, M. / Ellinger, B. / Witt, G. / Santarem, N. / Baptista, C. / Franco, C. / Moraes, C.B. / ...Authors: Linciano, P. / Pozzi, C. / Iacono, L.D. / di Pisa, F. / Landi, G. / Bonucci, A. / Gul, S. / Kuzikov, M. / Ellinger, B. / Witt, G. / Santarem, N. / Baptista, C. / Franco, C. / Moraes, C.B. / Muller, W. / Wittig, U. / Luciani, R. / Sesenna, A. / Quotadamo, A. / Ferrari, S. / Pohner, I. / Cordeiro-da-Silva, A. / Mangani, S. / Costantino, L. / Costi, M.P.
History
DepositionApr 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 8, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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)127,50418
Polymers122,6794
Non-polymers4,82514
Water15,421856
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20910 Å2
ΔGint-129 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.869, 90.373, 82.933
Angle α, β, γ (deg.)90.00, 115.68, 90.00
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 (E. coli) / References: UniProt: O76290

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Non-polymers , 5 types, 870 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-EUK / 6-[(3,4-dichlorophenyl)methylsulfanyl]-1,3-benzothiazol-2-amine


Mass: 341.279 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H10Cl2N2S2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.1 Å3/Da / Density % sol: 41.37 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2-2.5 M sodium acetate, 0.1 M sodium citrate, pH5

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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: Oct 21, 2017
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.52→67.48 Å / Num. obs: 149204 / % possible obs: 97.8 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.031 / Rrim(I) all: 0.062 / Net I/σ(I): 12.1
Reflection shellResolution: 1.52→1.6 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 21375 / CC1/2: 0.921 / Rpim(I) all: 0.259 / Rrim(I) all: 0.514 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDC

5jdc


Resolution: 1.52→67.48 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / Rfactor Rfree error: 0.075 / SU B: 1.833 / SU ML: 0.062 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / SU Rfree Cruickshank DPI: 0.075
RfactorNum. reflection% reflectionSelection details
Rfree0.19251 7581 5.1 %RANDOM
Rwork0.16616 ---
obs0.16752 141587 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: 1 / Resolution: 1.52→67.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7390 0 304 856 8550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0158126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.881.80311145
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25951070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49721.02294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.863151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2031547
X-RAY DIFFRACTIONr_chiral_restr0.1090.21115
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216016
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_it1.7581.7764105
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.72.6415136
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4132.0684021
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.48327.11413136
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.52→1.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 600 -
Rwork0.333 10227 -
obs--95.96 %

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