SAXSdb — 9uin

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Thioredoxin reductase 1, cytoplasmic

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 151–649 Chain B； UniProt 151–649	Mutation：SEC498C	TXP 1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 CU COPPER (II) ION × 6	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.03 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9UIN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CFY Crystal structure of human thioredoxin reductase 1 Deposited 2006-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–499（499 aa） Chain B 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；150 UL SITTING DROPS, 20% PEG3350, 0.1 M TRIS PH 7, ADDITIVE: NSDB-221	Resolution 2.70 Å R-free 0.248
2CFY Crystal structure of human thioredoxin reductase 1 Deposited 2006-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–499（499 aa） Chain D 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；150 UL SITTING DROPS, 20% PEG3350, 0.1 M TRIS PH 7, ADDITIVE: NSDB-221	Resolution 2.70 Å R-free 0.248
2CFY Crystal structure of human thioredoxin reductase 1 Deposited 2006-02-26	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–499（499 aa） Chain F 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；150 UL SITTING DROPS, 20% PEG3350, 0.1 M TRIS PH 7, ADDITIVE: NSDB-221	Resolution 2.70 Å R-free 0.248
2J3N X-ray structure of human thioredoxin reductase 1 Deposited 2006-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–499（499 aa） Chain B 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.287
2J3N X-ray structure of human thioredoxin reductase 1 Deposited 2006-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–499（499 aa） Chain D 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.287
2J3N X-ray structure of human thioredoxin reductase 1 Deposited 2006-08-22	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–499（499 aa） Chain F 1–499（499 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.287
2ZZ0 Crystal structure of human thioredoxin reductase I (SeCys 498 Cys) Deposited 2009-02-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 150–649（500 aa） Fragment：residues (-13)-499 Chain B 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.277
2ZZ0 Crystal structure of human thioredoxin reductase I (SeCys 498 Cys) Deposited 2009-02-02	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 150–649（500 aa） Fragment：residues (-13)-499 Chain D 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.80 Å R-free 0.277
2ZZB Crystal structure of human thioredoxin reductase I and terpyridine platinum(II) Deposited 2009-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 150–649（500 aa） Fragment：residues (-13)-499 Chain B 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 2 TPT 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, additive: 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.20 Å R-free 0.305
2ZZB Crystal structure of human thioredoxin reductase I and terpyridine platinum(II) Deposited 2009-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 150–649（500 aa） Fragment：residues (-13)-499 Chain D 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 SO4 SULFATE ION × 2 TPT 2,2':6',2''-TERPYRIDINE PLATINUM(II) Chloride × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M magnesium Sulfate, 0.05M MES, pH 6.0, additive: 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.20 Å R-free 0.305
2ZZC Crystal structure of NADP(H):human thioredoxin reductase I Deposited 2009-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 150–649（500 aa） Fragment：residues (-13)-499 Chain B 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M Magnesium Sulfate, 0.05M MES, pH 6.0, additive: 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.260
2ZZC Crystal structure of NADP(H):human thioredoxin reductase I Deposited 2009-02-09	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 150–649（500 aa） Fragment：residues (-13)-499 Chain D 150–649（500 aa） Fragment：residues (-13)-499	Mutation：SeCys498Cys Mutation：SeCys498Cys	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；5% PEG 3350, 0.005M Magnesium Sulfate, 0.05M MES, pH 6.0, additive: 20% 1,6 Hexanediol (0.001mL), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.60 Å R-free 0.260
3QFA Crystal structure of the human thioredoxin reductase-thioredoxin complex Deposited 2011-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–499（499 aa） Chain B 1–499（499 aa）	Mutation：C497S, U498C Mutation：C497S, U498C	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；297.15 K；15% PEG 6000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.15 K	Resolution 2.20 Å R-free 0.283
3QFB Crystal structure of the human thioredoxin reductase-thioredoxin complex Deposited 2011-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–499（499 aa） Chain B 1–499（499 aa）	Mutation：C497S, U498C Mutation：C497S, U498C	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；297.15 K；15% PEG 4000, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 297.15K	Resolution 2.60 Å R-free 0.297
7X1R Cryo-EM structure of human thioredoxin reductase bound by Au Deposited 2022-02-24	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 152–649（498 aa） Chain B 152–649（498 aa）	Not recorded	FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 AU GOLD ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRXR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–499； UniProt 151–649 Author chain B； PDBConstruct 1–499； UniProt 151–649

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9uin
Deposition date deposition_date	2025-04-15
Structure title title	Human thioredoxin reductase 1 (SeCys 498 Cys) with Cu(I)
Keywords keywords	Enzyme, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.39 Å
Radius of gyration Rg (electron density) rg_electron	31.95 Å
Forward intensity I(0) i0	192720000.00
Molecular weight molecular_weight	109820.0 kDa
Excluded volume excluded_volume	136960 Å³
Envelope volume envelope_volume	177490 Å³
Hydration-shell volume shell_volume	46211 Å³
Envelope diameter envelope_diameter	110.8 Å
Shell Rg shell_rg	39.10 Å
Envelope Rg envelope_rg	31.92 Å
Shape Rg shape_rg	31.97 Å
Total Rg total_rg	32.44 Å
Total atoms total_atoms	7690
Residues n_residues	968
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.0 Å
Rg (real space) rg_real	32.36 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.9270e+08
I(0) uncertainty (real space) i0_real_error	3.4370e+06
Rg (reciprocal space) rg_reciprocal	32.38 Å
I(0) (reciprocal space) i0_reciprocal	192700000.0000
Solution quality estimate total_estimate	0.8847
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.0 Å
Skewness Skewness skewness	0.360
Kurtosis Kurtosis kurtosis	-0.287
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	87520000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.925

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Thioredoxin reductase 1, cytoplasmic
Molecular weight formula_weight	54770.5 kDa
EC 编号 ec_number	1.8.1.9,1.11.1.2
Mutation mutation	SEC498C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	7690

MNGPEDLPKSYDYDLIIIGGGSGGLAAAKEAAQYGKKVMVLDFVTPTPLGTRWGLGGTCVNVGCIPKKLMHQAALLGQALQDSRNYGWKVEETVKHDWDRMIEAVQNHIGSLNWGYRVALREKKVVYENAYGQFIGPHRIKATNNKGKEKIYSAERFLIATGERPRYLGIPGDKEYCISSDDLFSLPYCPGKTLVVGASYVALECAGFLAGIGLDVTVMVRSILLRGFDQDMANKIGEHMEEHGIKFIRQFVPIKVEQIEAGTPGRLRVVAQSTNSEEIIEGEYNTVMLAIGRDACTRKIGLETVGVKINEKTGKIPVTDEEQTNVPYIYAIGDILEDKVELTPVAIQAGRLLAQRLYAGSTVKCDYENVPTTVFTPLEYGACGLSEEKAVEKFGEENIEVYHSYFWPLEWTIPSRDNNKCYAKIICNTKDNERVVGFHVLGPNAGEVTQGFAAALKCGLTKKQLDSTIGIHPVCAEVFTTLSVTKRSGASILQAGCCG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo

Entity 2 Entity 2 non-polymer

Description description	1,4,5,6-TETRAHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	747.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	6

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.03 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	63765

fit	/app/data/saxs_computation/ui/9uin/9uin.fit
pddf	/app/data/pr_computation/ui/9uin/9uin.pr.out
profile	/app/data/saxs_computation/ui/9uin/9uin.dat

Human thioredoxin reductase 1 (SeCys 498 Cys) with Cu(I)

1. Protein Identity and Related Structures Protein Identity & Related Structures

Thioredoxin reductase 1, cytoplasmic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D