5XCJ | pdb_00005xcj

Crystal structure of Vps29 single mutant (D62A) from Entamoeba histolytica

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5xcja_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	SCOPe (2.08)
B	d5xcjb_	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	automated matches	automated matches	(Entamoeba histolytica ) [TaxId: 5759 ],	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	8085937	3001067	SCOP2B (2022-06-29)
B	SCOP2 Family	YfcE-like	8085936	4002849	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Metallo-dependent phosphatases	8085937	3001067	SCOP2 (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	Jacalin	e5xcjA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Jacalin	ECOD (v294.1)
B	Jacalin	e5xcjB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Jacalin	ECOD (v294.1)

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)
B	3.60.21.10	Alpha Beta	4-Layer Sandwich	Purple Acid Phosphatase	chain A, domain 2	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Vacuolar protein sorting-associated protein 29	cation binding ion binding binding metal ion binding small molecule binding	cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization intercellular transport cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process establishment of protein localization protein transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization intercellular transport cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process establishment of protein localization protein transport macromolecule localization intracellular protein localization	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle protein-containing complex membrane membrane protein complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle protein-containing complex membrane membrane protein complex retromer complex endomembrane system

InterPro: Protein Family Classification InterPro Database Homepage

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

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.