5DPT

Crystal structure of PLEKHM1 LIR-fused human GABARAPL1_2-117

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5dpta_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5dptb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	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	Ubiquitin-like	8068228	3000157	SCOP2B (2022-06-29)
B	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)
A	Atg8	e5dptA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e5dptB1	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)
A	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	Pleckstrin homology domain-containing family M member 1, Gamma-aminobutyric acid receptor-associated protein-like 1,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 cation binding ion binding metal ion binding small molecule binding	catabolic process energy derivation by oxidation of organic compounds macroautophagy carbohydrate catabolic process autophagy macromolecule catabolic process cellular catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process process utilizing autophagic mechanism carbohydrate metabolic process glucan catabolic process glycogen metabolic process catabolic process energy derivation by oxidation of organic compounds macroautophagy carbohydrate catabolic process autophagy macromolecule catabolic process cellular catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process process utilizing autophagic mechanism carbohydrate metabolic process glucan catabolic process glycogen metabolic process cellular metabolic process primary metabolic process generation of precursor metabolites and energy glycophagy polysaccharide catabolic process metabolic process energy reserve metabolic process cellular process macromolecule metabolic process autophagy of mitochondrion 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 membrane organization transport membrane fusion organelle membrane fusion establishment of localization vesicle-mediated transport vesicle organization organelle fusion localization autophagosome-lysosome fusion vesicle fusion cellular localization late endosome to lysosome transport establishment of localization in cell vacuolar transport intracellular transport lysosomal transport organelle localization lysosome localization vacuolar localization protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of bone resorption regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization ruffle organization plasma membrane bounded cell projection assembly ruffle assembly positive regulation of cell projection organization positive regulation of cellular process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane vesicle membrane cytoplasmic vesicle organelle cytoplasm vesicle organelle membrane vacuole autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle Golgi apparatus endomembrane system cytosol polymeric cytoskeletal fiber cytoskeleton intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle endoplasmic reticulum nucleus membrane-enclosed lumen nucleolus intracellular organelle lumen organelle lumen nuclear lumen autolysosome lytic vacuole autolysosome membrane lytic vacuole membrane lysosomal membrane secondary lysosome lysosome endosome membrane endosome late endosome membrane late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B	IPR037213	RUN domain superfamily	Homologous Superfamily
A, B	IPR025258	Rubicon Homology Domain	Domain
A, B	IPR004012	RUN domain	Domain
A, B	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
A, B	IPR001849	Pleckstrin homology domain	Domain
A, B	IPR047326	PLEKHM1, RUN domain	Domain
A, B	IPR042827	PLEKHM1, PH domain	Domain
A, B	IPR011993	PH-like domain superfamily	Homologous Superfamily
A, B	IPR051366	Differentially Expressed in FDCP 8 Homolog	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q9Y4G2	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 osteopetrosis autosomal recessive osteopetrosis 6 allergic rhinitis endogenous depression osteosarcoma systemic lupus erythematosus atypical teratoid rhabdoid tumor large cell medulloblastoma Osteopetrosis - intermediate type ovarian cancer lung cancer osteopetrosis, autosomal dominant 3 ovarian carcinoma

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.