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- PDB-4new: Crystal structure of Trypanothione Reductase from Trypanosoma cru... -

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Basic information

Entry
Database: PDB / ID: 4new
TitleCrystal structure of Trypanothione Reductase from Trypanosoma cruzi in complex with inhibitor EP127 (5-{5-[1-(PYRROLIDIN-1-YL)CYCLOHEXYL]-1,3-THIAZOL-2-YL}-1H-INDOLE)
ComponentsTrypanothione reductase, putative
KeywordsOxidoreductase/Oxidoreductase inhibitor / Reductase / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


FAD/NAD-linked reductase, C-terminal dimerisation domain / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2JR / FLAVIN-ADENINE DINUCLEOTIDE / :
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPersch, E. / Bryson, S. / Pai, E.F. / Krauth-Siegel, R.L. / Diederich, F.
CitationJournal: Chemmedchem / Year: 2014
Title: Binding to large enzyme pockets: small-molecule inhibitors of trypanothione reductase.
Authors: Persch, E. / Bryson, S. / Todoroff, N.K. / Eberle, C. / Thelemann, J. / Dirdjaja, N. / Kaiser, M. / Weber, M. / Derbani, H. / Brun, R. / Schneider, G. / Pai, E.F. / Krauth-Siegel, R.L. / Diederich, F.
History
DepositionOct 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypanothione reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0733
Polymers53,9361
Non-polymers1,1372
Water00
1
A: Trypanothione reductase, putative
hetero molecules

A: Trypanothione reductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,1466
Polymers107,8712
Non-polymers2,2744
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_543x,-y-1,-z-3/21
Buried area9680 Å2
ΔGint-69 kcal/mol
Surface area37480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.846, 86.846, 151.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Trypanothione reductase, putative


Mass: 53935.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: TCSYLVIO_004807 / Production host: Escherichia coli (E. coli) / References: UniProt: K4E0T9
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-2JR / 5-{5-[1-(pyrrolidin-1-yl)cyclohexyl]-1,3-thiazol-2-yl}-1H-indole


Mass: 351.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N3S
Has protein modificationY
Sequence detailsAUTHORS HAVE INDICATED THAT THE RESIDUES ASN95 COULD NOT BE CLEARLY IDENTIFIED FROM THE ...AUTHORS HAVE INDICATED THAT THE RESIDUES ASN95 COULD NOT BE CLEARLY IDENTIFIED FROM THE INTERPRETATION OF THE ELECTRON DENSITY

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 298 K / pH: 8
Details: 0.1M TRIS, pH 8.0, 0.2M CaCl2, 20-22% PEG2000MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 9, 2013
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→17 Å / Num. obs: 14005 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 1.72 % / Rmerge(I) obs: 0.028
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 7.3 / % possible all: 75.4

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Processing

Software
NameClassification
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZL

1bzl


Resolution: 2.8→17 Å / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection
Rfree0.278 668
Rwork0.232 -
obs0.232 14005
all-14921
Refinement stepCycle: LAST / Resolution: 2.8→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 78 0 3787
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_chiral_restr
X-RAY DIFFRACTIONf_plane_restr

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