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- PDB-2wpf: Trypanosoma brucei trypanothione reductase in complex with 3,4- d... -

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Basic information

Entry
Database: PDB / ID: 2wpf
TitleTrypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00085762)
ComponentsTRYPANOTHIONE REDUCTASE
KeywordsOXIDOREDUCTASE / TRYPANOSOMIASIS / SLEEPING SICKNESS / FLAVOPROTEIN / REDOX-ACTIVE CENTER
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress ...trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glycosome / thioredoxin-disulfide reductase (NADPH) activity / ciliary plasm / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / nucleoplasm / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain ...Trypanothione reductase / : / Pyridine nucleotide-disulphide oxidoreductase, class I / FAD/NAD-linked reductase, C-terminal dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / FLAVIN-ADENINE DINUCLEOTIDE / Chem-WPF / Trypanothione reductase / Trypanothione reductase
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlphey, M.S. / Patterson, S. / Fairlamb, A.H.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Dihydroquinazolines as a Novel Class of Trypanosoma Brucei Trypanothione Reductase Inhibitors: Discovery, Synthesis, and Characterization of Their Binding Mode by Protein Crystallography.
Authors: Patterson, S. / Alphey, M.S. / Jones, D.C. / Shanks, E.J. / Street, I.P. / Frearson, J.A. / Wyatt, P.G. / Gilbert, I.H. / Fairlamb, A.H.
History
DepositionAug 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Refinement description / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRYPANOTHIONE REDUCTASE
B: TRYPANOTHIONE REDUCTASE
C: TRYPANOTHIONE REDUCTASE
D: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,04622
Polymers213,9924
Non-polymers5,05418
Water23,2931293
1
C: TRYPANOTHIONE REDUCTASE
D: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,51010
Polymers106,9962
Non-polymers2,5148
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10150 Å2
ΔGint-97.8 kcal/mol
Surface area36050 Å2
MethodPISA
2
A: TRYPANOTHIONE REDUCTASE
B: TRYPANOTHIONE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,53612
Polymers106,9962
Non-polymers2,54010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-129.1 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.820, 62.760, 167.440
Angle α, β, γ (deg.)90.00, 98.13, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.00429, 0.95509, 0.29629), (0.95593, -0.0909, 0.27917), (0.29357, 0.28203, -0.91339)-44.00228, -2.318, 157.60263
2given(-0.12645, 0.92237, 0.36502), (0.95281, 0.01057, 0.30338), (0.27597, 0.38616, -0.88018)-49.8005, 10.5444, 68.32908
3given(0.98617, 0.16285, 0.03084), (-0.16464, 0.98394, 0.06893), (-0.01912, -0.07306, 0.99714)-14.74194, -32.49897, 83.49995

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
TRYPANOTHIONE REDUCTASE


Mass: 53497.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI (eukaryote) / Strain: TREU927 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL
References: UniProt: P39051, UniProt: Q389T8*PLUS, trypanothione-disulfide reductase

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Non-polymers , 5 types, 1311 molecules

#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-WPF / 3-[(4S)-6-CHLORO-2-METHYL-4-(4-METHYLPHENYL)QUINAZOLIN-3(4H)-YL]-N,N-DIMETHYLPROPAN-1-AMINE


Mass: 355.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H26ClN3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1293 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.39 % / Description: NONE
Crystal growpH: 8
Details: 15MG/ML PROTEIN IN 25MM HEPES PH 7.5, 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG 3350, 40MM IMIDAZOLE PH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 9, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→19.9 Å / Num. obs: 160960 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WOI

2woi


Resolution: 1.9→19.888 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 4.39 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.156 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 8048 5 %RANDOM
Rwork0.1849 ---
obs0.188 160960 100 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.316 Å2
Baniso -1Baniso -2Baniso -3
1-0.789 Å20 Å20.452 Å2
2---0.299 Å20 Å2
3----0.362 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.888 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14837 0 322 1293 16452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02215554
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.98621164
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80451969
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89224.504615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075152547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8291570
X-RAY DIFFRACTIONr_chiral_restr0.1320.22378
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02111646
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2230.28608
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.210884
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21683
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.2119
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.264
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0791.59704
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.784215669
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.03535850
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5834.55486
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 562 -
Rwork0.342 10690 -
obs--100 %

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