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- PDB-5izc: Trypanosoma brucei PTR1 in complex with inhibitor F032 -

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Basic information

Entry
Database: PDB / ID: 5izc
TitleTrypanosoma brucei PTR1 in complex with inhibitor F032
Components(Pteridine reductase) x 2
KeywordsOXIDOREDUCTASE / Trypanosoma brucei / pteridine reductase / 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-6F4 / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pteridine reductase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsPozzi, C. / Landi, G. / Di Pisa, F. / Mangani, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
European Commission603240 Italy
CitationJournal: ACS Omega / Year: 2017
Title: Exploiting the 2-Amino-1,3,4-thiadiazole Scaffold To Inhibit Trypanosoma brucei Pteridine Reductase in Support of Early-Stage Drug Discovery.
Authors: Linciano, P. / Dawson, A. / Pohner, I. / Costa, D.M. / Sa, M.S. / Cordeiro-da-Silva, A. / Luciani, R. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Gribbon, P. / Reinshagen, J. / Wolf, ...Authors: Linciano, P. / Dawson, A. / Pohner, I. / Costa, D.M. / Sa, M.S. / Cordeiro-da-Silva, A. / Luciani, R. / Gul, S. / Witt, G. / Ellinger, B. / Kuzikov, M. / Gribbon, P. / Reinshagen, J. / Wolf, M. / Behrens, B. / Hannaert, V. / Michels, P.A.M. / Nerini, E. / Pozzi, C. / di Pisa, F. / Landi, G. / Santarem, N. / Ferrari, S. / Saxena, P. / Lazzari, S. / Cannazza, G. / Freitas-Junior, L.H. / Moraes, C.B. / Pascoalino, B.S. / Alcantara, L.M. / Bertolacini, C.P. / Fontana, V. / Wittig, U. / Muller, W. / Wade, R.C. / Hunter, W.N. / Mangani, S. / Costantino, L. / Costi, M.P.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 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)118,43816
Polymers114,3464
Non-polymers4,09212
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-133 kcal/mol
Surface area30500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.630, 89.443, 82.645
Angle α, β, γ (deg.)90.000, 115.870, 90.000
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: 28574.559 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Only in subunit C Cys60 has been oxidized to OCS. In all subunits Cys168 has been chemically modified by BME
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290, pteridine reductase
#2: Protein Pteridine reductase


Mass: 28622.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Only in subunit C Cys60 has been oxidized to OCS. In all subunits Cys168 has been chemically modified by BME
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O76290, pteridine reductase

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Non-polymers , 5 types, 585 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-6F4 / N~2~-[(thiophen-2-yl)methyl]-1,3,4-thiadiazole-2,5-diamine


Mass: 212.295 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8N4S2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / 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.: 573 / 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: 2.18 Å3/Da / Density % sol: 43.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: TbPTR1 6-10 mg/mL in 20 mM Tris-HCl pH 7.5 and 10 mM DTT or BME) and precipitant (1.5-2.5 M Sodium Acetate and 0.1 M Sodium Citrate pH 5)
PH range: 5.0 - 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 18, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→74.364 Å / Num. all: 73011 / Num. obs: 73011 / % possible obs: 98 % / Redundancy: 3 % / Rpim(I) all: 0.061 / Rrim(I) all: 0.108 / Rsym value: 0.089 / Net I/av σ(I): 6.025 / Net I/σ(I): 7.7 / Num. measured all: 217984
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.92-2.0230.3332196.9
2.02-2.1530.2472.6197.3
2.15-2.2930.1833.3197.6
2.29-2.482.80.1583.7197.8
2.48-2.722.80.1344.3198.4
2.72-3.043.10.096.4198.8
3.04-3.513.20.0629198.3
3.51-4.2930.04512.6198.5
4.29-6.072.90.03713.2199.4
6.07-44.7223.20.0358199.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WCD

4wcd


Resolution: 1.92→74.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.1 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.14
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 3668 5 %RANDOM
Rwork0.1611 ---
obs0.1633 69153 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.93 Å2 / Biso mean: 20.565 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.92→74.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 262 573 8127
Biso mean--23.5 29.55 -
Num. residues----985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197775
X-RAY DIFFRACTIONr_bond_other_d0.0030.027481
X-RAY DIFFRACTIONr_angle_refined_deg2.0212.00510629
X-RAY DIFFRACTIONr_angle_other_deg1.063.00217116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5545.031013
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53224.167288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.108151193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4271546
X-RAY DIFFRACTIONr_chiral_restr0.1040.21276
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218807
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021727
X-RAY DIFFRACTIONr_mcbond_it1.7631.8583968
X-RAY DIFFRACTIONr_mcbond_other1.7581.8573964
X-RAY DIFFRACTIONr_mcangle_it2.7082.7644943
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 247 -
Rwork0.241 5055 -
all-5302 -
obs--96.58 %

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