PDB-22ey: Crystal structure of thioredoxin gluthathione reductase from Schi...

ID or keywords:

Entry

Database: PDB / ID: 22ey

Title

Crystal structure of thioredoxin gluthathione reductase from Schistosoma japonicum SjTGR-WT

Components

thioredoxin-disulfide reductase (NADPH)

Keywords

OXIDOREDUCTASE / TGR

Function / homology

FLAVIN-ADENINE DINUCLEOTIDE

Function and homology information

Biological species

Schistosoma japonicum (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.557 Å

Authors

Wang, S.Q. / Huang, S.Q. / Lin, T.W.

Funding support

China, 1items

Citation

Journal: Plos Pathog. / Year: 2026
Title: Structural basis for substrate recognition and inhibition of thioredoxin glutathione reductase from Schistosoma japonicum: Implications for antiparasitic development.
Authors: Wang, S. / Hong, W. / Zhong, S. / Liang, Z. / Xiao, T. / Zhang, C. / Liu, X. / Dai, Z. / Li, Y. / Wu, S. / Cai, Q. / Wu, C. / Huang, Y. / Hong, P. / Ren, H. / Li, S. / Lin, T. / Chen, X. / Huang, S.

History

Deposition	Jan 8, 2026	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Apr 15, 2026	Provider: repository / Type: Initial release
Revision 1.1	May 6, 2026	Group: Structure summary / Category: entity / Item: _entity.details
Revision 1.2	May 27, 2026	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._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.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	22ey.cif.gz	245.9 KB	Display	PDBx/mmCIF format
PDB format	pdb22ey.ent.gz	188.9 KB	Display	PDB format
PDBx/mmJSON format	22ey.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/2e/22ey ftp://data.pdbj.org/pub/pdb/validation_reports/2e/22ey	HTTPS FTP

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Related structure data

Related structure data	22fcC 22fdC 22feC 22ffC 22fgC 22fhC 22fjC 22fkC 9lwmC 9lwzC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: thioredoxin-disulfide reductase (NADPH)

B: thioredoxin-disulfide reductase (NADPH)

hetero molecules

132 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	83.615, 86.266, 182.093
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
1	1	A
2	1	A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 6 - 595 / Label seq-ID: 6 - 595

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	thioredoxin-disulfide reductase (NADPH) Mass: 65160.949 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The penultimate amino acid, U, is selenocysteine. NCBI accession number is PZ269544.1 Source: (gene. exp.) Schistosoma japonicum (invertebrata) / Gene: EWB00_006158 Production host: synthetic Escherichia coli C321.deltaA (bacteria) References: thioredoxin-disulfide reductase (NADPH)
#2: Chemical	ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₇H₃₃N₉O₁₅P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.52 Å³/Da / Density % sol: 51.18 %
Crystal grow	Temperature: 295.15 K / Method: vapor diffusion, hanging drop / Details: 4% Tassimate (pH 6.5-8.0) and 15-20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.919082 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: May 31, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919082 Å / Relative weight: 1
Reflection	Resolution: 2.557→91.05 Å / Num. obs: 43384 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC_1/2: 0.988 / Net I/σ(I): 6.6
Reflection shell	Resolution: 2.557→2.69 Å / Num. unique obs: 6222 / CC_1/2: 0.366

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.557→91.047 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.886 / SU B: 13.893 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / ESU R: 0.798 / ESU R Free: 0.321
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2599	2157	4.993 %
R_work	0.2069	41047	-
all	0.21	-	-
obs	-	43204	99.537 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 50.865 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.508 Å²	0 Å²	-0 Å²
2-	-	1.351 Å²	-0 Å²
3-	-	-	-0.843 Å²

Refinement step

Cycle: LAST / Resolution: 2.557→91.047 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9056	0	106	14	9176

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	9387
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	8857
X-RAY DIFFRACTION	r_angle_refined_deg	1.656	1.819	12737
X-RAY DIFFRACTION	r_angle_other_deg	0.557	1.755	20471
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.174	5	1191
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	10.662	5	35
X-RAY DIFFRACTION	r_dihedral_angle_other_2_deg	0.024	10	2
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.58	10	1603
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.379	10	383
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	1446
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	10872
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2006
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1713
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.19	0.2	7644
X-RAY DIFFRACTION	r_nbtor_refined	0.178	0.2	4598
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.081	0.2	4904
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.185	0.2	152
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.225	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.208	0.2	54
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.168	0.2	4
X-RAY DIFFRACTION	r_mcbond_it	4.524	4.943	4758
X-RAY DIFFRACTION	r_mcbond_other	4.523	4.943	4757
X-RAY DIFFRACTION	r_mcangle_it	6.645	8.882	5951
X-RAY DIFFRACTION	r_mcangle_other	6.644	8.882	5952
X-RAY DIFFRACTION	r_scbond_it	4.899	5.276	4629
X-RAY DIFFRACTION	r_scbond_other	4.899	5.276	4630
X-RAY DIFFRACTION	r_scangle_it	7.315	9.536	6786
X-RAY DIFFRACTION	r_scangle_other	7.315	9.535	6787
X-RAY DIFFRACTION	r_lrange_it	9.433	48.431	10192
X-RAY DIFFRACTION	r_lrange_other	9.433	48.43	10193
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.077	0.05	17972

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.07704	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.07704	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.557-2.623	0.333	135	0.333	2924	X-RAY DIFFRACTION	96.8651
2.623-2.695	0.373	164	0.324	2886	X-RAY DIFFRACTION	98.6736
2.695-2.773	0.346	141	0.31	2823	X-RAY DIFFRACTION	99.4631
2.773-2.858	0.293	128	0.242	2770	X-RAY DIFFRACTION	99.759
2.858-2.952	0.278	140	0.246	2697	X-RAY DIFFRACTION	99.8241
2.952-3.055	0.314	152	0.243	2563	X-RAY DIFFRACTION	99.8162
3.055-3.17	0.268	130	0.215	2528	X-RAY DIFFRACTION	99.8873
3.17-3.3	0.294	165	0.23	2391	X-RAY DIFFRACTION	100
3.3-3.446	0.284	106	0.22	2357	X-RAY DIFFRACTION	100
3.446-3.614	0.229	117	0.197	2222	X-RAY DIFFRACTION	100
3.614-3.809	0.275	121	0.204	2114	X-RAY DIFFRACTION	99.9553
3.809-4.04	0.22	112	0.178	2010	X-RAY DIFFRACTION	99.9529
4.04-4.318	0.211	97	0.154	1902	X-RAY DIFFRACTION	100
4.318-4.663	0.201	100	0.143	1785	X-RAY DIFFRACTION	99.8411
4.663-5.107	0.236	102	0.156	1618	X-RAY DIFFRACTION	99.8839
5.107-5.708	0.243	72	0.171	1507	X-RAY DIFFRACTION	99.8735
5.708-6.586	0.254	58	0.178	1344	X-RAY DIFFRACTION	99.8576
6.586-8.056	0.161	53	0.14	1150	X-RAY DIFFRACTION	99.834
8.056-11.348	0.16	36	0.175	913	X-RAY DIFFRACTION	99.6849
11.348-91.047	0.463	28	0.35	543	X-RAY DIFFRACTION	98.4483

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