1PY1 | pdb_00001py1

Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d1py1b_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d1py1d_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1py1c_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1py1a_	All alpha proteins	alpha-alpha superhelix	ENTH/VHS domain	VHS domain	ADP-ribosylation factor binding protein Gga1	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	ENTH/VHS domain-like	8041836	3000164	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	ENTH/VHS domain-like	8041836	3000164	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	ENTH/VHS domain-like	8041836	3000164	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ENTH/VHS domain-like	8041836	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)
B		e1py1B1	A: alpha bundles	X: EGF-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (develop294)
D		e1py1D1	A: alpha bundles	X: EGF-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (develop294)
C		e1py1C1	A: alpha bundles	X: EGF-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (develop294)
A		e1py1A1	A: alpha bundles	X: EGF-like	H: tRNA-binding arm	T: tRNA-binding arm	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	Beta-secretase	amyloid-beta binding binding peptide binding peptidase activity omega peptidase activity catalytic activity, acting on a protein threonine-type peptidase activity hydrolase activity beta-aspartyl-peptidase activity catalytic activity endopeptidase activity aspartic-type peptidase activity aspartic-type endopeptidase activity protein binding amyloid-beta binding binding peptide binding peptidase activity omega peptidase activity catalytic activity, acting on a protein threonine-type peptidase activity hydrolase activity beta-aspartyl-peptidase activity catalytic activity endopeptidase activity aspartic-type peptidase activity aspartic-type endopeptidase activity protein binding protein serine/threonine kinase binding kinase binding enzyme binding protein kinase binding	trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling presynaptic modulation of chemical synaptic transmission chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling trans-synaptic signaling regulation of biological process regulation of signaling regulation of cellular process modulation of chemical synaptic transmission signaling biological regulation cell-cell signaling presynaptic modulation of chemical synaptic transmission chemical synaptic transmission cell communication synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication cellular process behavior multicellular organismal process locomotory behavior swimming behavior neuron apoptotic process positive regulation of programmed cell death regulation of apoptotic process positive regulation of biological process regulation of programmed cell death cell death positive regulation of apoptotic process apoptotic process positive regulation of neuron apoptotic process programmed cell death positive regulation of cellular process regulation of neuron apoptotic process startle response system process response to stimulus nervous system process regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus negative regulation of biological process prepulse inhibition response to external stimulus regulation of response to stimulus negative regulation of response to external stimulus amyloid precursor protein catabolic process metabolic process primary metabolic process protein metabolic process macromolecule metabolic process amyloid precursor protein metabolic process signaling receptor ligand precursor processing gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing amyloid-beta metabolic process response to hormone response to endogenous stimulus response to chemical response to insulin-like growth factor stimulus detection of external stimulus detection of mechanical stimulus involved in sensory perception of pain response to mechanical stimulus sensory perception of pain detection of mechanical stimulus involved in sensory perception sensory perception of mechanical stimulus detection of abiotic stimulus detection of stimulus sensory perception detection of mechanical stimulus response to abiotic stimulus detection of stimulus involved in sensory perception cellular component organization cellular component organization or biogenesis supramolecular fiber organization amyloid fibril formation cellular response to stimulus cellular response to metal ion cellular response to chemical stimulus response to metal ion cellular response to manganese ion response to manganese ion amyloid-beta formation response to copper ion cellular response to copper ion response to lead ion cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to amyloid-beta cellular response to oxygen-containing compound response to amyloid-beta membrane protein proteolysis membrane protein ectodomain proteolysis	cellular anatomical structure membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle vesicle lumen intracellular anatomical structure Golgi-associated vesicle lumen Golgi apparatus intracellular vesicle cellular anatomical structure membrane somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle vesicle lumen intracellular anatomical structure Golgi-associated vesicle lumen Golgi apparatus intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen organelle cytoplasm Golgi-associated vesicle vesicle Golgi apparatus subcompartment organelle subcompartment trans-Golgi network endoplasmic reticulum lumen endoplasmic reticulum endosome recycling endosome endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane cell body neuronal cell body axon transport vesicle synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle cell surface cell periphery plasma membrane membrane microdomain membrane raft late endosome multivesicular body lytic vacuole vacuole lysosome early endosome neuron to neuron synapse hippocampal mossy fiber to CA3 synapse
A, B, C, D	ADP-ribosylation factor binding protein GGA1	binding phospholipid binding lipid binding phosphatidylinositol binding small GTPase binding protein binding enzyme binding GTPase binding ubiquitin binding ubiquitin-like protein binding	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 localization to cell surface catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of metabolic process regulation of protein catabolic process intracellular transport establishment of localization in cell intracellular protein transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi protein localization to cilium protein localization to ciliary membrane protein localization to organelle	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen protein-containing complex early endosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle vesicle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network endosome membrane early endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR009120	Beta-secretase BACE1	Family
E, F, G, H	IPR033121	Peptidase family A1 domain	Domain
E, F, G, H	IPR033874	Memapsin-like	Domain
E, F, G, H	IPR001461	Aspartic peptidase A1	Family
E, F, G, H	IPR009119	Beta-secretase BACE	Family
E, F, G, H	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
E, F, G, H	IPR001969	Aspartic peptidase, active site	Active Site
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	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: P56817	Alzheimer disease pancreatic intraductal papillary-mucinous carcinoma Presenile dementia subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor lung cancer malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis toxic encephalopathy Crohn disease interstitial lung disease malignant ependymoma pancreatic ductal adenocarcinoma Alzheimer disease pancreatic intraductal papillary-mucinous carcinoma Presenile dementia subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor lung cancer malignant pancreatic neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm psoriasis toxic encephalopathy Crohn disease interstitial lung disease malignant ependymoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia schizophrenia amyloidosis dementia large cell medulloblastoma malignant mesothelioma osteosarcoma
A, B, C, D	Pharos: Q9UJY5	astrocytic tumor medulloblastoma ovarian cancer sarcoidosis malignant ependymoma oligodendroglioma primitive neuroectodermal tumor X-linked mixed deafness with perilymphatic gusher Malignant neoplasm of breast osteosarcoma psoriasis

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.