2D1I | pdb_00002d1i

Structure of human Atg4b

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B	d2d1ib_	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Autophagin-like	Cysteine protease ATG4B	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2d1ia1	Alpha and beta proteins (a+b)	Cysteine proteinases	Cysteine proteinases	Autophagin-like	Cysteine protease ATG4B	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)
B	SCOP2B Superfamily	Cysteine proteinases	8033717	3001808	SCOP2B (2022-06-29)
A	SCOP2 Family	Autophagin-like	8021337	4002557	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cysteine proteinases	8033717	3001808	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Peptidase_C54	e2d1iB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C54	ECOD (1.6)
A	Peptidase_C54	e2d1iA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C54	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF20166	ATG4, F-type LIR motif (ATG4_LIR)	ATG4, F-type LIR motif	-	Motif
A, B	PF03416	Peptidase C54 catalytic domain (Peptidase_C54)	Peptidase C54 catalytic domain	This is the catalytic domain of of cysteine peptidases from C54 family, which includes cysteine protease ATG4 from human and its homologues from fungi and plants. ATG4 plays a key role in cytoplasm to vacuole transport (Cvt) and autophagy by mediati ...	This is the catalytic domain of of cysteine peptidases from C54 family, which includes cysteine protease ATG4 from human and its homologues from fungi and plants. ATG4 plays a key role in cytoplasm to vacuole transport (Cvt) and autophagy by mediating both proteolytic activation and delipidation of ATG8 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Cysteine protease APG4B	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity scaffold protein binding protein binding binding protein-phosphatidylethanolamide deconjugating activity	developmental process ear development sensory organ development animal organ development tissue development otolith mineralization otolith development otolith mineralization completed early in development inner ear development anatomical structure development biomineral tissue development autophagosome assembly catabolic process organelle assembly developmental process ear development sensory organ development animal organ development tissue development otolith mineralization otolith development otolith mineralization completed early in development inner ear development anatomical structure development biomineral tissue development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular process metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism piecemeal microautophagy of the nucleus microautophagy nucleophagy localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization aggrephagy primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing protein metabolic process macromolecule metabolic process macromolecule modification protein delipidation protein modification process mitophagy autophagy of mitochondrion protein localization to phagophore assembly site	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cytoplasmic vesicle intracellular vesicle vesicle vacuolar membrane autophagosome membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol cytoplasmic vesicle intracellular vesicle vesicle vacuolar membrane autophagosome membrane membrane vacuole autophagosome bounding membrane of organelle organelle membrane endoplasmic reticulum endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005078	Peptidase C54	Family
A, B	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B	IPR046792	Peptidase C54, catalytic domain	Domain
A, B	IPR046793	Cysteine protease ATG4, F-type LIR motif	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y4P1	allergic rhinitis breast carcinoma ovarian cancer asthma inflammatory bowel disease psoriasis brain glioma osteosarcoma

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.