5GTU

Structural and mechanistic insights into regulation of the retromer coat by TBC1d5

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	d5gtua1	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5gtua2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	Metallo-dependent phosphatases	8036532	3001067	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	Metallophos_2	e5gtuA1	A: a+b four layers	X: Carbon-nitrogen hydrolase-like	H: Metallo-dependent phosphatases (From Topology)	T: Metallo-dependent phosphatases	F: Metallophos_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12850	Calcineurin-like phosphoesterase superfamily domain (Metallophos_2)	Calcineurin-like phosphoesterase superfamily domain	Members of this family are part of the Calcineurin-like phosphoesterase superfamily.	Domain
B	PF00566	Rab-GTPase-TBC domain (RabGAP-TBC)	Rab-GTPase-TBC domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport vesicle-mediated transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane membrane protein complex retromer complex retromer, cargo-selective complex cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane late endosome
B	TBC1 domain family member 5	protein-containing complex binding binding retromer complex binding AP-2 adaptor complex binding GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity	cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy cellular process metabolic process process utilizing autophagic mechanism cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell protein localization establishment of protein localization nitrogen compound transport organic substance transport protein transport cellular macromolecule localization macromolecule localization regulation of localization import into cell regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization receptor internalization positive regulation of biological process regulation of receptor internalization cellular component organization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis positive regulation of cellular process regulation of endocytosis regulation of biological process regulation of transport regulation of receptor-mediated endocytosis biological regulation regulation of vesicle-mediated transport positive regulation of receptor internalization positive regulation of transport endocytosis receptor-mediated endocytosis response to nutrient levels response to stimulus response to stress response to starvation	membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle vacuole autophagosome cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex membrane membrane protein complex retromer complex endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure organelle vacuole autophagosome cytoplasm cellular anatomical entity intracellular membrane-bounded organelle protein-containing complex membrane membrane protein complex retromer complex endomembrane system Golgi apparatus cytosol endosome membrane endosome intracellular vesicle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle vesicle organelle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000979	Phosphodiesterase MJ0936/Vps29	Family
A	IPR024654	Calcineurin-like phosphoesterase domain, lpxH-type	Domain
A	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
A	IPR028661	Vacuolar protein sorting-associated protein 29	Family
B	IPR035969	Rab-GAP-TBC domain superfamily	Homologous Superfamily
B	IPR000195	Rab-GAP-TBC domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q9UBQ0	breast carcinoma ovarian cancer hereditary spastic paraplegia pancreatic ductal adenocarcinoma malignant pancreatic neoplasm
B	Pharos: Q92609	astrocytic tumor Gaucher disease medulloblastoma osteosarcoma rheumatoid arthritis attention deficit hyperactivity disorder, inattentive type large cell medulloblastoma myocardial infarction ovarian cancer Tourette syndrome atypical teratoid rhabdoid tumor lymphoplasmacytic lymphoma oligodendroglioma psoriasis tuberculosis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.