5b6m

Crystal structure of human peroxiredoxin 6 in reduced state

Method: X-RAY DIFFRACTION

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

Peroxiredoxin-6

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PRDX6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–224； UniProt 1–224 Author chain B； PDBConstruct 1–224； UniProt 1–224 Author chain C； PDBConstruct 1–224； UniProt 1–224 Author chain D； PDBConstruct 1–224； UniProt 1–224 Author chain E； PDBConstruct 1–224； UniProt 1–224 Author chain F； PDBConstruct 1–224； UniProt 1–224

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	5b6m
Deposition date deposition_date	2016-05-30
Structure title title	Crystal structure of human peroxiredoxin 6 in reduced state
Keywords keywords	Prx6, 1-Cys Prx, Catalytic site, Oxidation, Reduction, OXIDOREDUCTASE; 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.

5b6m__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5b6m__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5b6m__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	23.66 Å
Rg (electron density)	22.45 Å
Total Rg	23.43 Å
Atom count	3505
Residues	444
Excluded volume	63165 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5b6m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5b6m__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5b6m__assembly_3__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 (2)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5b6ma_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d5b6mb_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d5b6mc_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d5b6md_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d5b6me_
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.47.1.10 — Glutathione peroxidase-like

Domain ID domain_id	d5b6mf_
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.47.1.10 — Glutathione peroxidase-like

CATH v4.4 (12 domains)

Domain ID domain_id	5b6mA01
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	5b6mA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	5b6mB01
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	5b6mB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	5b6mC01
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	5b6mC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	5b6mD01
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	5b6mD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	5b6mE01
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	5b6mE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

Domain ID domain_id	5b6mF01
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	5b6mF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1020 — Antioxidant, Horf6; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Antioxidant, Horf6; Chain A, domain2

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Unit-cell length a length_a	94.353 Å
Unit-cell length b length_b	106.349 Å
Unit-cell length c length_c	165.504 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	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.496 Å
Low-resolution limit resolution_low	37.893 Å
R factor r_factor	0.2350
R_work r_work	0.2331
R_free r_free	0.2896

Description description	Peroxiredoxin-6
Molecular weight formula_weight	25068.0 kDa
EC 编号 ec_number	1.11.1.15
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10485

Crystal structure of human peroxiredoxin 6 in reduced state

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

Peroxiredoxin-6

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

5b6m__assembly_3__model_1

5b6m__assembly_3__model_1 | I(q)

5b6m__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli-Pichia pastoris shuttle vector pPpARG4

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	124

Crystal structure of human peroxiredoxin 6 in reduced state

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

Peroxiredoxin-6

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

5b6m__assembly_3__model_1

5b6m__assembly_3__model_1 | I(q)

5b6m__assembly_3__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

7. Citations (1)