2cfy

Crystal structure of human thioredoxin reductase 1

Method: X-RAY DIFFRACTION Dmax: 199.3 Å Quality: GOOD

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 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
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 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
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 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

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.

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 23–521; UniProt 1–499 Author chain B; PDBConstruct 23–521; UniProt 1–499 Author chain C; PDBConstruct 23–521; UniProt 1–499 Author chain D; PDBConstruct 23–521; UniProt 1–499 Author chain E; PDBConstruct 23–521; UniProt 1–499 Author chain F; PDBConstruct 23–521; 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 2cfy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2cfy
Deposition date deposition_date2006-02-26
Structure title titleCrystal structure of human thioredoxin reductase 1
Keywords keywordsOXIDOREDUCTASE, PHOSPHORYLATION, REDOX-ACTIVE CENTER, NADP; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier55.80
Radius of gyration Rg (electron density) rg_electron56.56
Forward intensity I(0) i01416470000.00
Molecular weight molecular_weight316090.0 kDa
Excluded volume excluded_volume396280 ų
Envelope volume envelope_volume552050 ų
Hydration-shell volume shell_volume87493 ų
Envelope diameter envelope_diameter216.2
Shell Rg shell_rg52.84
Envelope Rg envelope_rg55.69
Shape Rg shape_rg56.58
Total Rg total_rg56.39
Total atoms total_atoms22240
Residues n_residues2904
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax199.3
Rg (real space) rg_real56.40
Rg uncertainty (real space) rg_real_error2.39
I(0) (real space) i0_real1.4160e+09
I(0) uncertainty (real space) i0_real_error3.1190e+07
Rg (reciprocal space) rg_reciprocal55.30
I(0) (reciprocal space) i0_reciprocal1414000000.0000
Solution quality estimate total_estimate0.7928
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary49.8
Skewness Skewness skewness0.638
Kurtosis Kurtosis kurtosis-0.139
Angular range angular_range— – 0.1400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha180800000.0000
Real-space data points n_real_points29
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.637; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.842; Smooth: 0.555

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 18 domains

CATH v4.4 (18 domains)

Domain ID domain_id2cfyA01
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_id2cfyA02
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_id2cfyA03
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_id2cfyB01
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_id2cfyB02
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_id2cfyB03
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_id2cfyC01
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_id2cfyC02
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_id2cfyC03
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_id2cfyD01
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_id2cfyD02
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_id2cfyD03
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_id2cfyE01
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_id2cfyE02
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_id2cfyE03
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_id2cfyF01
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_id2cfyF02
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_id2cfyF03
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

8. Citations (1)

9. Files and Curves (10)