6TL0 | pdb_00006tl0

Solution structure and 1H, 13C and 15N chemical shift assignments for the complex of VPS29 with VARP 687-747

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d6tl0a1	Alpha and beta proteins (a+b)	Metallo-dependent phosphatases	Metallo-dependent phosphatases	YfcE-like	Vacuolar protein sorting 29, VPS29	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d6tl0a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	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	8035118	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	e6tl0A1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Metallophos_2	ECOD (v294.1)

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	PF12796	Ankyrin repeats (3 copies) (Ank_2)	Ankyrin repeats (3 copies)	-	Repeat

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	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 post-Golgi vesicle-mediated transport vesicle-mediated 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 post-Golgi vesicle-mediated transport vesicle-mediated transport Golgi to vacuole transport vacuolar transport Golgi vesicle transport endosomal transport cytosolic transport retrograde transport, endosome to Golgi localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system retromer, cargo-selective complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system retromer, cargo-selective complex membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle cytosol endosome membrane cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane organelle membrane
B	Ankyrin repeat domain-containing protein 27	small GTPase binding protein binding binding enzyme binding GTPase 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 SNARE binding guanyl-nucleotide exchange factor activity	localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization nervous system development generation of neurons anatomical structure morphogenesis neuron development cellular process cellular response to stimulus cellular localization pigment cell differentiation response to stimulus developmental pigmentation cellular pigmentation endosome to pigment granule transport pigmentation establishment of localization in cell cellular pigment accumulation endosome to melanosome transport pigment accumulation intracellular transport response to external stimulus developmental maturation pigment granule maturation regulation of neuron projection development regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process positive regulation of neuron projection development positive regulation of cell projection organization positive regulation of cellular process regulation of biological process regulation of cell projection organization biological regulation regulation of plasma membrane bounded cell projection organization regulation of localization membrane fusion organelle membrane fusion negative regulation of biological process regulation of vesicle fusion negative regulation of vesicle fusion negative regulation of transport vesicle-mediated transport vesicle organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly negative regulation of cellular process protein-containing complex assembly SNARE complex assembly negative regulation of SNARE complex assembly membrane organization negative regulation of cellular component organization regulation of transport protein-containing complex organization regulation of vesicle-mediated transport regulation of cellular component biogenesis regulation of organelle organization negative regulation of protein-containing complex assembly organelle fusion organelle organization regulation of SNARE complex assembly negative regulation of organelle organization vesicle fusion endosomal transport vesicle-mediated transport between endosomal compartments early endosome to late endosome transport positive regulation of nervous system development regulation of cell differentiation regulation of neurogenesis regulation of cell morphogenesis regulation of cell development positive regulation of developmental process regulation of dendrite morphogenesis positive regulation of cell development positive regulation of cell morphogenesis regulation of dendrite development positive regulation of multicellular organismal process regulation of developmental process regulation of nervous system development positive regulation of cell differentiation dendrite development positive regulation of neurogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis regulation of multicellular organismal development positive regulation of dendrite morphogenesis dendrite morphogenesis cell morphogenesis involved in neuron differentiation localization within membrane endocytic recycling vesicle-mediated transport to the plasma membrane	cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol cellular anatomical structure membrane membrane-bounded organelle intracellular anatomical structure pigment granule intracellular vesicle intracellular membrane-bounded organelle intracellular organelle melanosome cytoplasmic vesicle organelle cytoplasm vesicle cytosol cell periphery plasma membrane transport vesicle endomembrane system lytic vacuole vacuole lysosome endosome tubular endosome cell projection neuron projection plasma membrane bounded cell projection cytoplasmic vesicle membrane vesicle membrane organelle membrane early endosome late endosome

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	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
B	IPR003123	VPS9 domain	Domain
B	IPR002110	Ankyrin repeat	Repeat
B	IPR051248	UPF0507/Ankyrin repeat domain-containing protein 27	Family
B	IPR037191	VPS9 domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q96NW4	eosinophilic esophagitis bipolar disorder malignant glioma myopathy dermatomyositis glioblastoma malignant mesothelioma ovarian cancer endogenous depression lymphoplasmacytic lymphoma medulloblastoma pancreatic ductal adenocarcinoma

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.