SAXSdb — 3pin

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

Thioredoxin-2

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peptide methionine sulfoxide reductase × 1 （P40029） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRX2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–104； UniProt 1–104

Peptide methionine sulfoxide reductase

Saccharomyces cerevisiae

UniProt P40029

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Thioredoxin-2 × 1 （P22803） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MSRA_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–183； UniProt 2–184

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	3pin
Deposition date deposition_date	2010-11-07
Structure title title	Crystal structure of Mxr1 from Saccharomyces cerevisiae in complex with Trx2
Keywords keywords	methionine-S-sulfoxide reductase, thioredoxin, ELECTRON TRANSPORT-Oxidoreductase complex; ELECTRON TRANSPORT/Oxidoreductase
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.

3pin__assembly_1__model_1

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

Download this curve (.dat)

3pin__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pin__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.89 Å
Rg (electron density)	20.28 Å
Total Rg	21.17 Å
Atom count	1924
Residues	243
Excluded volume	34426 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pin__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	Thioredoxin-2
Molecular weight formula_weight	11197.8 kDa
Mutation mutation	C34S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1939

MVTQLKSASEYDSALASGDKLVVVDFFATWCGPSKMIAPMIEKFAEQYSDAAFYKLDVDEVSDVAQKAEVSSMPTLIFYKGGKEVTRVVGANPAAIKQAIASNV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptide methionine sulfoxide reductase
Molecular weight formula_weight	20975.4 kDa
EC 编号 ec_number	1.8.4.11
Mutation mutation	C23S, C25S, C44S, C68S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SSLISKTIKYDPAKDKLITLASGSFWGTEHMYRKYLNDRIVDSKVGYANGEESKKDSPSSVSYKRVSGGDTDFAEVLQVSYNPKVITLRELTDFFFRIHDPTTSNSQGPDKGTQYRSGLFAHSDADLKELAKIKEEWQPKWGNKIATVIEPIKNFYDAEEYHQLYLDKNPQGYACPTHYLREM

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	yeast
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3pina_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.0 — automated matches

Domain ID domain_id	d3pinb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.28 — Peptide methionine sulfoxide reductase
Family Family family	d.58.28.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3pinA00
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	3pinB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1060 — Peptide Methionine Sulfoxide Reductase; Chain A
Homologous superfamily homologous superfamily	10 — Peptide methionine sulphoxide reductase MsrA

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Unit-cell length a length_a	122.266 Å
Unit-cell length b length_b	122.266 Å
Unit-cell length c length_c	122.266 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2366
R_work r_work	0.2344
R_free r_free	0.2788

Crystal structure of Mxr1 from Saccharomyces cerevisiae in complex with Trx2

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

Thioredoxin-2

State in the Current Structure

Other States of the Same Protein in the Database

Peptide methionine sulfoxide reductase

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

3pin__assembly_1__model_1

3pin__assembly_1__model_1 | I(q)

3pin__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Mxr1 from Saccharomyces cerevisiae in complex with Trx2

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

Thioredoxin-2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peptide methionine sulfoxide reductase

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

3pin__assembly_1__model_1

3pin__assembly_1__model_1 | I(q)

3pin__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)