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2j3n

X-ray structure of human thioredoxin reductase 1

Method: X-RAY DIFFRACTION Dmax: 198.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

THIOREDOXIN REDUCTASE 1

HOMO SAPIENS

UniProt Q16881

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 1–499 Chain B； UniProt 1–499 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 experimental conditions Resolution 2.80 Å R-free 0.287
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 1–499 Chain D； UniProt 1–499 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 experimental conditions Resolution 2.80 Å R-free 0.287
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 1–499 Chain F； UniProt 1–499 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 experimental conditions Resolution 2.80 Å R-free 0.287

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 2J3N 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 ligand/ion 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 ligand/ion 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 ligand/ion 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
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 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 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 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 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 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 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion Different experimental method Different experimental conditions 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
9UIN Human thioredoxin reductase 1 (SeCys 498 Cys) with Cu(I) Deposited 2025-04-15 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 151–649（499 aa）
Chain B 151–649（499 aa）
Mutation：SEC498C 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

8 other PDB entries and 13 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 21–519； UniProt 1–499 Author chain B； PDBConstruct 21–519； UniProt 1–499 Author chain C； PDBConstruct 21–519； UniProt 1–499 Author chain D； PDBConstruct 21–519； UniProt 1–499 Author chain E； PDBConstruct 21–519； UniProt 1–499 Author chain F； PDBConstruct 21–519； UniProt 1–499

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2j3n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2j3n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2j3n
Deposition date deposition_date2006-08-22
Structure title titleX-ray structure of human thioredoxin reductase 1
Keywords keywords;FAD, NADP, HUMAN, SELENIUM, CYTOPLASM, FLAVOPROTEIN, REDOX REGULATION, ELECTRON TRANSPORT, OXIDOREDUCTASE, SELENOCYSTEINE, PHOSPHORYLATION, PYRIDINE NUCLEOTIDE DEPENDENT DISULFIDE REDUCTASE, REDOX-ACTIVE CENTER ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.55 Å
Radius of gyration Rg (electron density) rg_electron56.30 Å
Forward intensity I(0) i01594700000.00
Molecular weight molecular_weight331240.0 kDa
Excluded volume excluded_volume413830 ų
Envelope volume envelope_volume561620 ų
Hydration-shell volume shell_volume88798 ų
Envelope diameter envelope_diameter212.8 Å
Shell Rg shell_rg53.00 Å
Envelope Rg envelope_rg55.58 Å
Shape Rg shape_rg56.30 Å
Total Rg total_rg56.20 Å
Total atoms total_atoms23250
Residues n_residues2931
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax198.4 Å
Rg (real space) rg_real56.12 Å
Rg uncertainty (real space) rg_real_error2.84 Å
I(0) (real space) i0_real1.5950e+09
I(0) uncertainty (real space) i0_real_error3.6510e+07
Rg (reciprocal space) rg_reciprocal55.07 Å
I(0) (reciprocal space) i0_reciprocal1592000000.0000
Solution quality estimate total_estimate0.7961
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.6 Å
Skewness Skewness skewness0.630
Kurtosis Kurtosis kurtosis-0.149
Angular range angular_range— – 0.1400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha179900000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.639; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.581
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id2j3nA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nA02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
Domain ID domain_id2j3nB01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nB02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
Domain ID domain_id2j3nC01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nC02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nC03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
Domain ID domain_id2j3nD01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nD02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nD03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
Domain ID domain_id2j3nE01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nE02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nE03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
Domain ID domain_id2j3nF01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nF02
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id2j3nF03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily30 — FAD/NAD-linked reductase, C-terminal dimerisation domain
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8. Citations (1)

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9. Files and Curves (10)