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- PDB-2yhi: Trypanosoma brucei PTR1 in complex with inhibitor WH16 -

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Basic information

Entry
Database: PDB / ID: 2yhi
TitleTrypanosoma brucei PTR1 in complex with inhibitor WH16
Components(PTERIDINE REDUCTASE, ...) x 2
KeywordsOXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE
Function / homology
Function and homology information


pteridine reductase / pteridine reductase activity / oxidoreductase activity / nucleotide binding / cytosol
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 / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE / Pteridine reductase, putative
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNerini, E. / Dawson, A. / Hunter, W.N. / Costi, M.P.
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
DepositionMay 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 23, 2012Provider: 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PTERIDINE REDUCTASE, PUTATIVE
B: PTERIDINE REDUCTASE, PUTATIVE
C: PTERIDINE REDUCTASE, PUTATIVE
D: PTERIDINE REDUCTASE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,07418
Polymers122,7114
Non-polymers4,36314
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21870 Å2
ΔGint-153.8 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.280, 90.740, 84.290
Angle α, β, γ (deg.)90.00, 115.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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PTERIDINE REDUCTASE, ... , 2 types, 4 molecules ACBD

#1: Protein PTERIDINE REDUCTASE, PUTATIVE / PTR1


Mass: 30685.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CYS 59 OXIDIZED TO S-OXY CYSTEINE / Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET15B_TBPTR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581W1, pteridine reductase
#2: Protein PTERIDINE REDUCTASE, PUTATIVE / PTR1


Mass: 30669.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Plasmid: PET15B_TBPTR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q581W1, pteridine reductase

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Non-polymers , 7 types, 550 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-W16 / 5-(2-CHLOROETHYL)-1,3,4-THIADIAZOL-2-AMINE


Mass: 163.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6ClN3S
#5: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#8: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsN TERMINAL TAG SEQUENCE INCLUDED.

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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: 41.2 % / Description: NONE
Crystal growpH: 7.5
Details: RESERVOIR CONDITIONS: 100 MM SODIUM CITRATE PH 5, 1.8 M SODIUM ACETATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Oct 4, 2009 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→31.41 Å / Num. obs: 87904 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.7 / % possible all: 88.4

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X9G

2x9g


Resolution: 1.8→31.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.576 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.135 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20716 4413 5 %RANDOM
Rwork0.17864 ---
obs0.18009 83470 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.36 Å2
2--2.12 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7418 0 268 536 8222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227872
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.172.00410698
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3175984
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.41524.397307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71151259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4771548
X-RAY DIFFRACTIONr_chiral_restr0.0690.21292
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215752
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_it0.4551.54969
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.87427963
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.332903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0954.52733
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 301 -
Rwork0.308 5663 -
obs--87.09 %

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