1LF8 | pdb_00001lf8

Complex of GGA3-VHS Domain and CI-MPR C-terminal Phosphopeptide

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)
D	d1lf8d1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1lf8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1lf8c_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1lf8b1	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1lf8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1lf8a_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga3	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)
D	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ENTH/VHS domain-like	8037388	3000164	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)
D		e1lf8D1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
C		e1lf8C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
B		e1lf8B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)
A		e1lf8A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Propep_M14	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
C	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
B	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)
A	1.25.40.90	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00790	VHS domain (VHS)	VHS domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Cation-independent mannose-6-phosphate receptor	insulin-like growth factor binding protein binding binding growth factor binding phosphoprotein binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding G-protein alpha-subunit binding insulin-like growth factor receptor activity molecular transducer activity catalytic activity, acting on a protein kinase activity insulin-like growth factor binding protein binding binding growth factor binding phosphoprotein binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding G-protein alpha-subunit binding insulin-like growth factor receptor activity molecular transducer activity catalytic activity, acting on a protein kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity catalytic activity retinoic acid binding organic acid binding isoprenoid binding retinoid binding ion binding anion binding lipid binding carboxylic acid binding monocarboxylic acid binding identical protein binding protein-containing complex binding retromer complex binding insulin-like growth factor II binding enzyme binding	developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process developmental process spermatogenesis sexual reproduction reproductive process multicellular organismal reproductive process developmental process involved in reproduction male gamete generation gamete generation regulation of biological process positive regulation of programmed cell death regulation of cellular process regulation of apoptotic process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process cellular process apoptotic process programmed cell death positive regulation of cellular process biological process involved in interspecies interaction between organisms host-mediated perturbation of viral process modulation of process of another organism host-mediated activation of viral process host-mediated perturbation of symbiont process localization import into cell transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development response to retinoic acid response to lipid response to stimulus response to chemical response to oxygen-containing compound cellular response to stimulus signaling signal transduction cell communication cellular localization establishment of localization in cell vacuolar transport intracellular transport lysosomal transport animal organ regeneration regeneration G protein-coupled receptor signaling pathway post-embryonic development response to tetrachloromethane	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle nucleus membrane-enclosed lumen endomembrane system intracellular organelle lumen organelle envelope lumen organelle envelope organelle lumen nuclear envelope lumen nuclear envelope Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network Golgi membrane perinuclear region of cytoplasm endosome membrane endosome anchoring junction cell junction focal adhesion cell-substrate junction cell surface cell periphery plasma membrane transport vesicle early endosome trans-Golgi network transport vesicle Golgi-associated vesicle secretory granule secretory vesicle secretory granule membrane trans-Golgi network membrane clathrin coat membrane coat protein-containing complex membrane protein complex coated membrane late endosome
A, B, C, D	ADP-ribosylation factor binding protein GGA3	binding phospholipid binding lipid binding phosphatidylinositol binding small GTPase binding protein binding enzyme binding GTPase binding ubiquitin binding ubiquitin-like protein binding protein-containing complex binding protein transporter activity transporter activity	Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane Golgi to plasma membrane transport establishment of protein localization cellular localization protein localization to cell periphery post-Golgi vesicle-mediated transport transport establishment of protein localization to membrane protein localization to plasma membrane establishment of protein localization to plasma membrane Golgi to plasma membrane protein transport localization within membrane protein localization to membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization protein transport macromolecule localization cellular process intracellular protein localization Golgi vesicle transport protein destabilization regulation of protein stability biological regulation regulation of biological quality protein localization to cell surface catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process intracellular transport establishment of localization in cell intracellular protein transport amyloid precursor protein catabolic process regulation of cellular process regulation of amyloid-beta formation negative regulation of biological process regulation of amyloid precursor protein catabolic process regulation of primary metabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process negative regulation of cellular process amyloid precursor protein metabolic process negative regulation of protein metabolic process amyloid-beta formation negative regulation of macromolecule metabolic process negative regulation of amyloid-beta formation regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process in the vacuole positive regulation of protein metabolic process positive regulation of biological process lysosomal protein catabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of lysosomal protein catabolic process positive regulation of cellular process protein catabolic process in the vacuole regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of lysosomal protein catabolic process positive regulation of protein catabolic process in the vacuole regulation of protein catabolic process protein targeting establishment of protein localization to vacuole protein localization to vacuole lysosomal transport protein localization to lysosome establishment of protein localization to organelle protein targeting to lysosome protein localization to organelle vacuolar transport protein targeting to vacuole endocytic recycling endosomal transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome protein-containing complex endosome membrane membrane endosome membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle lytic vacuole vacuole cytoplasm intracellular membrane-bounded organelle lysosome protein-containing complex endosome membrane membrane endosome intracellular vesicle recycling endosome endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle recycling endosome membrane vesicle membrane cytoplasmic vesicle vesicle organelle membrane Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network early endosome early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR000562	Fibronectin type II domain	Domain
E, F, G, H	IPR009011	Mannose-6-phosphate receptor binding domain superfamily	Homologous Superfamily
E, F, G, H	IPR044865	MRH domain	Domain
E, F, G, H	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
E, F, G, H	IPR000479	Cation-independent mannose-6-phosphate receptor repeat	Repeat
E, F, G, H	IPR013806	Kringle-like fold	Homologous Superfamily
A, B, C, D	IPR046996	GGA3, VHS domain	Domain
A, B, C, D	IPR002014	VHS domain	Domain
A, B, C, D	IPR008942	ENTH/VHS	Homologous Superfamily
A, B, C, D	IPR041198	N-terminal extension of GAT domain	Domain
A, B, C, D	IPR044111	GGA3, GAT domain	Domain
A, B, C, D	IPR008153	Gamma-adaptin ear (GAE) domain	Domain
A, B, C, D	IPR038425	GAT domain superfamily	Homologous Superfamily
A, B, C, D	IPR013041	Clathrin adaptor, appendage, Ig-like subdomain superfamily	Homologous Superfamily
A, B, C, D	IPR004152	GAT domain	Domain
A, B, C, D	IPR008152	Clathrin adaptor, alpha/beta/gamma-adaptin, appendage, Ig-like subdomain	Domain
A, B, C, D	IPR027422	ADP-ribosylation factor-binding protein GGA1-3	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E, F, G, H	Pharos: P11717	Alzheimer disease Parkinson disease congenital diaphragmatic hernia prostate cancer hepatocellular carcinoma Liver Cirrhosis, Experimental Lewy body dementia lung disease malignant pancreatic neoplasm myopathy ovarian cancer spondyloarthropathy endomyocardial fibrosis heart disease juvenile dermatomyositis Alzheimer disease Parkinson disease congenital diaphragmatic hernia prostate cancer hepatocellular carcinoma Liver Cirrhosis, Experimental Lewy body dementia lung disease malignant pancreatic neoplasm myopathy ovarian cancer spondyloarthropathy endomyocardial fibrosis heart disease juvenile dermatomyositis MALT lymphoma nephrolithiasis pancreatic ductal adenocarcinoma Pick disease psoriasis exocrine pancreatic carcinoma tuberculosis large cell medulloblastoma lysosomal storage disease mucopolysaccharidosis type 2 osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia plasma cell myeloma prostate carcinoma chronic kidney disease rheumatoid arthritis
A, B, C, D	Pharos: Q9NZ52	Malignant neoplasm of breast systemic lupus erythematosus non-alcoholic fatty liver disease systemic sclerosis osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H	SEP	Parent Component: SER RESID: AA0037 PSI-MOD : O-phospho-L-serine MOD:00046

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.