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- PDB-9s3h: Crystal structure of Cryptosporidium parvum Thioredoxin Reductase... -

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Basic information

Entry
Database: PDB / ID: 9s3h
TitleCrystal structure of Cryptosporidium parvum Thioredoxin Reductase in complex with Auranofin
ComponentsThioredoxin reductase
KeywordsFLAVOPROTEIN / reductase
Function / homology
Function and homology information


glutathione-disulfide reductase (NADPH) activity / thioredoxin-disulfide reductase (NADPH) / thioredoxin-disulfide reductase (NADPH) activity / cell redox homeostasis / glutathione metabolic process / flavin adenine dinucleotide binding / cellular response to oxidative stress / mitochondrion / cytosol
Similarity search - Function
Thioredoxin/glutathione reductase selenoprotein / : / Pyridine nucleotide-disulphide oxidoreductase, class I / 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 / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
: / FLAVIN-ADENINE DINUCLEOTIDE / Thioredoxin reductase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.28 Å
AuthorsGabriele, F. / Palerma, M. / Ardini, M. / Bogard, J. / Ippoliti, R. / Williams, D.L. / Angelucci, F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Gold-containing compounds target an apicomplexan Thioredoxin reductase: Disclosing reactivity through structural and functional characterization.
Authors: Gabriele, F. / Palerma, M. / Bogard, J. / Paluzzi, L. / Zineddu, S. / Geri, A. / Vitali, V. / Massai, L. / Ardini, M. / Bellelli, A. / Petukhov, P.A. / Ippoliti, R. / Messori, L. / Williams, D.L. / Angelucci, F.
History
DepositionJul 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2833
Polymers56,3001
Non-polymers9832
Water00
1
A: Thioredoxin reductase
hetero molecules

A: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,5666
Polymers112,6012
Non-polymers1,9654
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area11220 Å2
ΔGint-81 kcal/mol
Surface area37410 Å2
Unit cell
Length a, b, c (Å)72.523, 72.523, 184.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Thioredoxin reductase


Mass: 56300.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: TRx / Production host: Escherichia coli (E. coli) / References: UniProt: C8CCG0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-AU / GOLD ION


Mass: 196.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Au / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Tris/HCl, 0.1 M KSCN, PEG 2000 MME,

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.28→46.98 Å / Num. obs: 8155 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.998 / Net I/σ(I): 15.9
Reflection shellResolution: 3.28→3.54 Å / Num. unique obs: 523 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.28→46.98 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / SU B: 83.713 / SU ML: 0.6 / Cross valid method: THROUGHOUT / ESU R Free: 0.7 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29632 394 4.9 %RANDOM
Rwork0.23671 ---
obs0.23987 7690 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.896 Å2
Baniso -1Baniso -2Baniso -3
1--3.67 Å2-0 Å2-0 Å2
2---3.67 Å2-0 Å2
3---7.35 Å2
Refinement stepCycle: 1 / Resolution: 3.28→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3784 0 54 0 3838
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0133943
X-RAY DIFFRACTIONr_bond_other_d0.0050.0163731
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.6385348
X-RAY DIFFRACTIONr_angle_other_deg1.0851.5788628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6395507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87423.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.55215659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2931516
X-RAY DIFFRACTIONr_chiral_restr0.0450.2523
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024809
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02844
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 3.28→3.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 31 -
Rwork0.334 550 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 32.4765 Å / Origin y: -16.7143 Å / Origin z: 7.4898 Å
111213212223313233
T0.4029 Å2-0.1637 Å20.1467 Å2-0.3807 Å20.0617 Å2--0.1127 Å2
L3.6407 °2-0.9418 °2-1.1038 °2-2.7369 °20.7144 °2--2.368 °2
S0.0597 Å °0.0705 Å °-0.0326 Å °0.337 Å °0.1893 Å °0.2682 Å °0.0749 Å °-0.6044 Å °-0.249 Å °

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