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- PDB-1gxf: CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN... -

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Basic information

Entry
Database: PDB / ID: 1gxf
TitleCRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI TRYPANOTHIONE REDUCTASE IN COMPLEX WITH THE INHIBITOR QUINACRINE MUSTARD
ComponentsTRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
KeywordsOXIDOREDUCTASE / TRYPANOTHIONE REDUCTASE / FAD DEPENDENT / DISULPHIDE OXIDOREDUCTASE / QUINACRINE MUSTARD / INHIBITOR / REDOX-ACTIVE CENTER / FLAVOPROTEIN / FAD / NADP
Function / homology
Function and homology information


trypanothione-disulfide reductase / trypanothione-disulfide reductase (NADPH) activity / glutathione-disulfide reductase (NADPH) activity / glutathione metabolic process / cell redox homeostasis / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
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
FLAVIN-ADENINE DINUCLEOTIDE / MALEIC ACID / QUINACRINE MUSTARD / Trypanothione reductase
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsBond, C.S. / Peterson, M.R. / Vickers, T.J. / Fairlamb, A.H. / Hunter, W.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Two Interacting Binding Sites for Quinacrine Derivatives in the Active Site of Trypanothione Reductase: A Template for Drug Design
Authors: Saravanamuthu, A. / Vickers, T.J. / Bond, C.S. / Peterson, M.R. / Hunter, W.N. / Fairlamb, A.H.
History
DepositionApr 4, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

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Assembly

Deposited unit
A: TRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
B: TRYPANOTHIONE REDUCTASE (OXIDIZED FORM)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,4149
Polymers107,8512
Non-polymers3,5637
Water95553
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-80.17 kcal/mol
Surface area36730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.100, 93.100, 156.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.979689, 0.200521, 0.000849), (0.200248, 0.978116, 0.05648), (0.010495, 0.055503, -0.998403)
Vector: 84.3337, -8.5127, -0.3716)

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Components

#1: Protein TRYPANOTHIONE REDUCTASE (OXIDIZED FORM) / N(1) / N(8)-BIS(GLUTATHIONYL)SPERMIDINE REDUCTASE


Mass: 53925.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: COVALENTLY LABELLED WITH QUINACRINE MUSTARD / Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: BRAZILIAN SILVIO STRAIN CLONE X10/1 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P28593, EC: 1.6.4.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-MAE / MALEIC ACID


Mass: 116.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4O4
#4: Chemical
ChemComp-QUM / QUINACRINE MUSTARD / N-{(1S)-4-[BIS(2-CHLOROETHYL)AMINO]-1-METHYLBUTYL}-N-(6-CHLORO-2-METHOXY-9-ACRIDINYL)AMINE


Mass: 468.847 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H28Cl3N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTRYPANOTHIONE IS THE PARASITE ANALOG OF GLUTATHIONE AND THIS ENZYME IS THE EQUIVALENT OF ...TRYPANOTHIONE IS THE PARASITE ANALOG OF GLUTATHIONE AND THIS ENZYME IS THE EQUIVALENT OF GLUTATHIONE REDUCTASE.
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: 3.17 Å3/Da / Density % sol: 61 %
Crystal growpH: 6 / Details: MALEIC BUFFER, PEG 4000, pH 6.00

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→21 Å / Num. obs: 29073 / % possible obs: 79 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.9 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.6 / % possible all: 82

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TYT

1tyt


Resolution: 2.7→21 Å / SU B: 11.848 / SU ML: 0.25126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.3924
Details: THE MISSING N- AND C-TERMINAL RESIDUES COULD NOT BE SEEN IN THE ELECTRON DENSITY MAP CLEARLY
RfactorNum. reflection% reflection
Rfree0.25 1023 5 %
Rwork0.19 --
obs-29073 79 %
Displacement parametersBiso mean: 46 Å2
Refinement stepCycle: LAST / Resolution: 2.7→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7445 0 228 53 7726

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