SAXSdb — 3wgx

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

Thioredoxin domain-containing protein 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peroxiredoxin-4 × 1 （O08807） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peroxiredoxin-4 × 1 （O08807） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TXND5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–113； UniProt 190–298 Author chain B； PDBConstruct 5–113； UniProt 190–298

Peroxiredoxin-4

OrganismNot specified

UniProt O08807

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin domain-containing protein 5 × 1 （Q8NBS9） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin domain-containing protein 5 × 1 （Q8NBS9） GLYCEROL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRDX4_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–20； UniProt 244–263 Author chain D； PDBConstruct 1–20； UniProt 244–263

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	3wgx
Deposition date deposition_date	2013-08-13
Structure title title	Crystal structure of ERp46 Trx2 in a complex with Prx4 C-term
Keywords keywords	PDI family member, thioredoxin domain, protein disulfide isomerase, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3wgx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3wgx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wgx__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	14.82 Å
Rg (electron density)	13.25 Å
Total Rg	14.61 Å
Atom count	949
Residues	118
Excluded volume	16776 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wgx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wgx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Thioredoxin domain-containing protein 5
Molecular weight formula_weight	12975.6 kDa
Mutation mutation	C220A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2461

GSHMGLYELSASNFELHVAQGDHFIKFFAPWCGHAKALAPTWEQLALGLEHSETVKIGKVDCTQHYELCSGNQVRGYPTLLWFRDGKKVDQYKGKRDLESLREYVESQLQRTE

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peroxiredoxin-4
Molecular weight formula_weight	2092.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

HGEVCPAGWKPGSETIIPDP

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	388

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3wgxA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	3wgxB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

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Unit-cell length a length_a	35.098 Å
Unit-cell length b length_b	36.406 Å
Unit-cell length c length_c	40.594 Å
Unit-cell angle α angle_alpha	81.17 °
Unit-cell angle β angle_beta	87.47 °
Unit-cell angle γ angle_gamma	85.40 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	0.920 Å
Low-resolution limit resolution_low	26.785 Å
R factor r_factor	0.1405
R_work r_work	0.1396
R_free r_free	0.1580

Crystal structure of ERp46 Trx2 in a complex with Prx4 C-term

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

Thioredoxin domain-containing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Peroxiredoxin-4

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3wgx__assembly_2__model_1

3wgx__assembly_2__model_1 | I(q)

3wgx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of ERp46 Trx2 in a complex with Prx4 C-term

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

Thioredoxin domain-containing protein 5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peroxiredoxin-4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3wgx__assembly_2__model_1

3wgx__assembly_2__model_1 | I(q)

3wgx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)