5B6N

Crystal structures of human peroxiredoxin 6 in sulfinic acid state

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5b6na_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5b6nb_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5b6nc_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5b6nd_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5b6ne_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d5b6nf_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	1-Cys peroxiredoxin	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Thioredoxin-like	8057898	3000031	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	AhpC-TSA_1	e5b6nA1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
B	AhpC-TSA_1	e5b6nB1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
C	AhpC-TSA_1	e5b6nC1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
D	AhpC-TSA_1	e5b6nD1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
E	AhpC-TSA_1	e5b6nE1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
F	AhpC-TSA_1	e5b6nF1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
D	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
E	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)
F	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
F	3.30.1020.10	Alpha Beta	2-Layer Sandwich	Antioxidant, Horf6	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00578	AhpC/TSA family (AhpC-TSA)	AhpC/TSA family	This family contains proteins related to alkyl hydroperoxide reductase (AhpC) and thiol specific antioxidant (TSA).	Domain
A, B, C, D, E A, B, C, D, E, F	PF10417	C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx_C)	C-terminal domain of 1-Cys peroxiredoxin	This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding al ...	This is the C-terminal domain of 1-Cys peroxiredoxin (1-cysPrx), a member of the peroxiredoxin superfamily which protect cells against membrane oxidation through glutathione (GSH)-dependent reduction of phospholipid hydroperoxides to corresponding alcohols [1]. The C-terminal domain is crucial for providing the extra cysteine necessary for dimerisation of the whole molecule. Loss of the enzyme's peroxidase activity is associated with oxidation of the catalytic cysteine, upstream of this domain; and glutathionylation, presumably through its disruption of protein structure, facilitates access for GSH, resulting in spontaneous reduction of the mixed disulfide to the sulfhydryl and consequent activation of the enzyme [2]. The domain is associated with family AhpC-TSA, Pfam:PF00578, which carries the catalytic cysteine.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Peroxiredoxin-6	phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase activity 1-acylglycerophosphocholine O-acyltransferase activity O-acyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity peroxidase activity oxidoreductase activity phospholipase A2 activity hydrolase activity, acting on ester bonds carboxylic ester hydrolase activity hydrolase activity catalytic activity phospholipase activity lipase activity 1-acylglycerophosphocholine O-acyltransferase activity O-acyltransferase activity acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity peroxidase activity oxidoreductase activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor glutathione peroxidase activity peroxiredoxin activity cell adhesion molecule binding cadherin binding protein binding binding calcium-independent phospholipase A2 activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding identical protein binding	cell redox homeostasis cellular homeostasis homeostatic process response to oxidative stress response to stimulus response to stress cellular response to stimulus cellular detoxification cellular response to chemical stimulus response to chemical detoxification cellular process cellular oxidant detoxification cellular response to toxic substance cell redox homeostasis cellular homeostasis homeostatic process response to oxidative stress response to stimulus response to stress cellular response to stimulus cellular detoxification cellular response to chemical stimulus response to chemical detoxification cellular process cellular oxidant detoxification cellular response to toxic substance response to toxic substance lipid catabolic process catabolic process phospholipid catabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process primary metabolic process phospholipid metabolic process organophosphate metabolic process phosphate-containing compound metabolic process glycerophospholipid catabolic process metabolic process glycerolipid metabolic process phosphorus metabolic process lipid metabolic process regulation of cellular process regulation of mRNA splicing, via spliceosome mRNA processing positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of metabolic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process RNA processing regulation of biological process positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of mRNA processing regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of mRNA splicing, via spliceosome positive regulation of biological process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of mRNA processing RNA splicing biological regulation regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of RNA splicing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process RNA splicing, via transesterification reactions positive regulation of gene expression mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile regulation of mRNA metabolic process positive regulation of RNA splicing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle cytosol lytic vacuole intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen organelle lumen secretory granule primary lysosome secretory vesicle perinuclear region of cytoplasm nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR019479	Peroxiredoxin, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR024706	Peroxiredoxin, AhpC-type	Family
A, B, C, D, E A, B, C, D, E, F	IPR013766	Thioredoxin domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR045020	1-Cys peroxiredoxin	Family
A, B, C, D, E A, B, C, D, E, F	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR000866	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F	Pharos: P30041	Down syndrome adult acute respiratory distress syndrome contact dermatitis rheumatoid arthritis systemic lupus erythematosus ulcerative colitis Contact hypersensitivity lung benign neoplasm myopathy plasma cell myeloma schizophrenia breast fibroadenoma coronary artery disease hepatocellular carcinoma lung cancer Down syndrome adult acute respiratory distress syndrome contact dermatitis rheumatoid arthritis systemic lupus erythematosus ulcerative colitis Contact hypersensitivity lung benign neoplasm myopathy plasma cell myeloma schizophrenia breast fibroadenoma coronary artery disease hepatocellular carcinoma lung cancer medulloblastoma ovarian cancer psoriasis spina bifida myocardial ischemia pancreatic ductal adenocarcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, B, C, D, E A, B, C, D, E, F	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.