3TKP | pdb_00003tkp

Crystal structure of full-length human peroxiredoxin 4 in the reduced form

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
E	d3tkpe_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3tkpd_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3tkpc_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3tkpb_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3tkpa_	Alpha and beta proteins (a/b)	Thioredoxin fold	Thioredoxin-like	Glutathione peroxidase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E	AhpC-TSA_1	e3tkpE1	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	e3tkpD1	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	e3tkpC1	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	e3tkpB1	A: a+b three layers	X: Thioredoxin-like	H: Thioredoxin-like (From Topology)	T: Thioredoxin-like	F: AhpC-TSA_1	ECOD (1.6)
A	AhpC-TSA_1	e3tkpA1	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)
E	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
D	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
C	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
B	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)
A	3.40.30.10	Alpha Beta	3-Layer(aba) Sandwich	Glutaredoxin	Glutaredoxin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	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	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	Peroxiredoxin-4	peroxidase activity oxidoreductase activity thioredoxin-dependent peroxiredoxin activity antioxidant activity oxidoreductase activity, acting on peroxide as acceptor thioredoxin peroxidase activity catalytic activity peroxiredoxin activity molecular sequestering activity molecular adaptor activity identical protein binding protein binding binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development catabolic process hydrogen peroxide metabolic process reactive oxygen species metabolic process metabolic process cellular process hydrogen peroxide catabolic process spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation cellular component organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization negative regulation of male germ cell proliferation regulation of cellular process regulation of reproductive process regulation of male germ cell proliferation negative regulation of biological process germ cell proliferation regulation of germ cell proliferation negative regulation of cellular process regulation of multicellular organismal process regulation of biological process negative regulation of cell population proliferation cell population proliferation biological regulation male germ cell proliferation negative regulation of reproductive process regulation of cell population proliferation negative regulation of multicellular organismal process negative regulation of germ cell proliferation cell redox homeostasis cellular homeostasis homeostatic process cellular response to stimulus response to stimulus signaling intracellular signal transduction cell communication phosphate-containing compound metabolic process intracellular signaling cassette protein metabolic process signal transduction protein modification process phosphorus metabolic process I-kappaB phosphorylation protein phosphorylation phosphorylation primary metabolic process canonical NF-kappaB signal transduction macromolecule modification macromolecule metabolic process biosynthetic process gene expression macromolecule biosynthetic process protein maturation response to oxidative stress response to stress	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol membrane-enclosed lumen intracellular vesicle ficolin-1-rich granule intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle organelle lumen cytoplasmic vesicle ficolin-1-rich granule lumen secretory granule secretory vesicle vesicle lumen cytoplasmic vesicle lumen secretory granule lumen nucleus endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR019479	Peroxiredoxin, C-terminal	Domain
A, B, C, D, E	IPR050217	Thiol-specific antioxidant peroxiredoxin	Family
A, B, C, D, E	IPR013766	Thioredoxin domain	Domain
A, B, C, D, E	IPR036249	Thioredoxin-like superfamily	Homologous Superfamily
A, B, C, D, E	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	Pharos: Q13162	diffuse large B-cell lymphoma hyperglycemia allergic contact dermatitis glucose intolerance malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma acute myeloid leukemia astrocytic tumor diabetes mellitus Disease Progression interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm diffuse large B-cell lymphoma hyperglycemia allergic contact dermatitis glucose intolerance malignant glioma oligodendroglioma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma acute myeloid leukemia astrocytic tumor diabetes mellitus Disease Progression interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm Sjogren syndrome atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant ependymoma medulloblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis amyotrophic lateral sclerosis breast cancer intellectual disability lung cancer

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.