6krp

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant

Method: X-RAY DIFFRACTION

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

Peroxiredoxin

Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	CITRIC ACID × 10 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TDXH_AERPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 1–250 Author chain B； PDBConstruct 1–250； UniProt 1–250 Author chain C； PDBConstruct 1–250； UniProt 1–250 Author chain D； PDBConstruct 1–250； UniProt 1–250 Author chain E； PDBConstruct 1–250； UniProt 1–250 Author chain F； PDBConstruct 1–250； UniProt 1–250 Author chain G； PDBConstruct 1–250； UniProt 1–250 Author chain H； PDBConstruct 1–250； UniProt 1–250 Author chain I； PDBConstruct 1–250； UniProt 1–250 Author chain J； PDBConstruct 1–250； UniProt 1–250

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	6krp
Deposition date deposition_date	2019-08-22
Structure title title	Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant
Keywords keywords	Peroxiredoxin, 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.

6krp__assembly_1__model_1

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

Download this curve (.dat)

6krp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6krp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.82 Å
Rg (electron density)	50.85 Å
Total Rg	51.09 Å
Atom count	19752
Residues	2437
Excluded volume	351550 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6krp__assembly_1__model_1`	decameric （10）	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	Peroxiredoxin
Molecular weight formula_weight	28580.7 kDa
EC 编号 ec_number	1.11.1.15
Mutation mutation	C50S,W88A,C207S,C213S
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	21385

MPGSIPLIGERFPEMEVTTDHGVIKLPDHYVSQGKWFVLFSHPADFTPVSTTEFVSFARRYEDFQRLGVDLIGLSVDSVFSHIKWKEAIERHIGVRIPFPIIADPQGTVARRLGLLHAESATHTVRGVFIVDARGVIRTMLYYPMELGRLVDEILRIVKALKLGDSLKRAVPADWPNNEIIGEGLIVPPPTTEDQARARMESGQYRSLDWWFSWDTPASRDDVEEARRYLRRAAEKPAKLLYEEARTHLH

Source Source

Source organism organism	Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)
NCBI taxonomy ID ncbi_taxonomy_id	272557
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1633

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d6krpa_
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	d6krpb_
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	d6krpc_
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	d6krpd_
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	d6krpe_
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	d6krpf_
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	d6krpg_
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	d6krph_
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	d6krpi_
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	d6krpj_
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 (20 domains)

Domain ID domain_id	6krpA01
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	6krpA02
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	6krpB01
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	6krpB02
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	6krpC01
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	6krpC02
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	6krpD01
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	6krpD02
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	6krpE01
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	6krpE02
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	6krpF01
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	6krpF02
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	6krpG01
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	6krpG02
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	6krpH01
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	6krpH02
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	6krpI01
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	6krpI02
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	6krpJ01
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	6krpJ02
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	76.240 Å
Unit-cell length b length_b	103.285 Å
Unit-cell length c length_c	105.129 Å
Unit-cell angle α angle_alpha	105.78 °
Unit-cell angle β angle_beta	105.25 °
Unit-cell angle γ angle_gamma	92.45 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	49.368 Å
R factor r_factor	—
R_work r_work	0.1639
R_free r_free	0.1883

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant

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

Peroxiredoxin

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

6krp__assembly_1__model_1

6krp__assembly_1__model_1 | I(q)

6krp__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Peroxiredoxin from Aeropyrum pernix K1 (ApPrx) 0Cys W88A mutant

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

Peroxiredoxin

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

6krp__assembly_1__model_1

6krp__assembly_1__model_1 | I(q)

6krp__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)