8ESE | pdb_00008ese

Crystal structure of human Vps29 bound to a peptide from Vps35L

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)
B [auth Z]	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)
B [auth Z]	Iso_dh	e8eseZ1	A: a/b three-layered sandwiches	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: Iso_dh	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth Z]	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth Z]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Z]	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport vesicle-mediated transport endosomal transport intercellular 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 intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle cytoplasm vesicle protein-containing complex membrane-bounded organelle intracellular anatomical structure early endosome endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure 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
A [auth X]	VPS35 endosomal protein-sorting factor-like	-	Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization cellular process Golgi vesicle transport intracellular transport endocytic recycling endosomal transport Golgi to plasma membrane transport cellular localization post-Golgi vesicle-mediated transport transport localization within membrane establishment of localization vesicle-mediated transport vesicle-mediated transport to the plasma membrane localization cellular process Golgi vesicle transport intracellular transport endocytic recycling endosomal transport establishment of localization in cell establishment of protein localization protein transport macromolecule localization intracellular protein localization	membrane-bounded organelle intracellular anatomical structure ficolin-1-rich granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle ficolin-1-rich granule endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane membrane-bounded organelle intracellular anatomical structure ficolin-1-rich granule membrane membrane intracellular vesicle intracellular membrane-bounded organelle ficolin-1-rich granule endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane cell periphery plasma membrane endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth Z]	IPR000979	Phosphodiesterase MJ0936/Vps29	Family
B [auth Z]	IPR024654	Calcineurin-like phosphoesterase domain, lpxH-type	Domain
B [auth Z]	IPR029052	Metallo-dependent phosphatase-like	Homologous Superfamily
B [auth Z]	IPR028661	Vacuolar protein sorting-associated protein 29	Family
A [auth X]	IPR029705	VPS35 endosomal protein sorting factor-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth Z]	Pharos: Q9UBQ0	breast carcinoma ovarian cancer hereditary spastic paraplegia pancreatic ductal adenocarcinoma malignant pancreatic neoplasm
A [auth X]	Pharos: Q7Z3J2	Alzheimer disease malignant mesothelioma tuberculosis large cell medulloblastoma osteosarcoma malignant colon neoplasm ovarian cancer

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.