5LXH | pdb_00005lxh

GABARAP-L1 ATG4B LIR Complex

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ubiquitin-like	8068228	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8068228	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8068228	3000157	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)
C	Atg8	e5lxhC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e5lxhB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
A	Atg8	e5lxhA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth E], E [auth F], F [auth G]	Cysteine protease ATG4B	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
A, B, C	Gamma-aminobutyric acid receptor-associated protein-like 1	phosphatidylethanolamine binding binding phospholipid binding lipid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding Tat protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cytoskeletal protein binding beta-tubulin binding phosphatidylethanolamine binding binding phospholipid binding lipid binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor binding Tat protein binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding cytoskeletal protein binding beta-tubulin binding tubulin binding signaling receptor binding GABA receptor binding	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization autophagosome maturation cellular component organization or biogenesis cellular response to stimulus response to nutrient levels cellular response to nitrogen levels response to stimulus cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly mitophagy autophagy of mitochondrion	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane cell projection cilium plasma membrane bounded cell projection vacuole autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle Golgi apparatus endomembrane system cytosol cell periphery plasma membrane intracellular membraneless organelle ciliary basal body microtubule organizing center cytoskeleton membraneless organelle microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth E], E [auth F], F [auth G]	IPR005078	Peptidase C54	Family
D [auth E], E [auth F], F [auth G]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
D [auth E], E [auth F], F [auth G]	IPR046792	Peptidase C54, catalytic domain	Domain
D [auth E], E [auth F], F [auth G]	IPR046793	Cysteine protease ATG4, F-type LIR motif	Conserved Site
A, B, C	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B, C	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth E], E [auth F], F [auth G]	Pharos: Q9Y4P1	allergic rhinitis breast carcinoma ovarian cancer asthma inflammatory bowel disease psoriasis brain glioma osteosarcoma
A, B, C	Pharos: Q9H0R8	malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor acute myeloid leukemia transitional cell carcinoma breast cancer ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma lung adenocarcinoma malignant ependymoma MALT lymphoma osteosarcoma pilocytic astrocytoma malignant pancreatic neoplasm oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm primitive neuroectodermal tumor acute myeloid leukemia transitional cell carcinoma breast cancer ductal breast carcinoma in situ gastric cancer hepatocellular carcinoma lung adenocarcinoma malignant ependymoma MALT lymphoma osteosarcoma pilocytic astrocytoma psoriasis astrocytic tumor tuberculosis breast carcinoma endometriosis gastric carcinoma invasive ductal breast carcinoma lung cancer malignant glioma medulloblastoma ovarian cancer pituitary cancer subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor dermatomyositis exocrine pancreatic carcinoma glioblastoma large cell medulloblastoma malignant colon neoplasm

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.