2YPS | pdb_00002yps

Crystal structure of the PX domain of human sorting nexin 3

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d2ypsd_	Alpha and beta proteins (a+b)	PX domain	PX domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d2ypsc_	Alpha and beta proteins (a+b)	PX domain	PX domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2ypsb_	Alpha and beta proteins (a+b)	PX domain	PX domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ypsa1	Alpha and beta proteins (a+b)	PX domain	PX domain	automated matches	automated matches	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2ypsa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	HTH_24	e2ypsD2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (develop294)
C	AsnC_trans_reg_3	e2ypsC3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: AsnC_trans_reg_3	ECOD (develop294)
B	HTH_24	e2ypsB2	A: alpha bundles	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: HTH_24	ECOD (develop294)
A	DNA_pol_B_exo1	e2ypsA1	A: alpha bundles	X: Ribonuclease H-like	H: Ribonuclease H-like	T: Ribonuclease H-like	F: DNA_pol_B_exo1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (4.3.0)
C	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (4.3.0)
B	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (4.3.0)
A	3.30.1520.10	Alpha Beta	2-Layer Sandwich	PX Domain	Phox-like domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00787	PX domain (PX)	PX domain	PX domains bind to phosphoinositides.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	SORTING NEXIN-3	phosphatidylinositol-3,5-bisphosphate binding ion binding binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding protein-containing complex binding retromer complex binding protein phosphatase binding phosphatase binding phosphatidylinositol-3,5-bisphosphate binding ion binding binding anion binding phosphatidylinositol bisphosphate binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding small molecule binding protein-containing complex binding retromer complex binding protein phosphatase binding phosphatase binding protein binding enzyme binding phosphatidylinositol-4-phosphate binding phosphatidylinositol-5-phosphate binding phosphatidylinositol-3-phosphate binding	cellular process membrane docking protein to membrane docking cellular localization transport intracellular transport late endosome to Golgi transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process membrane docking protein to membrane docking cellular localization transport intracellular transport late endosome to Golgi transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell Golgi vesicle transport membrane organization cellular component organization membrane invagination cellular component organization or biogenesis establishment of protein localization protein transport macromolecule localization intracellular protein localization biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus host-mediated suppression of symbiont invasion host-mediated perturbation of symbiont process response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus modulation of process of another organism regulation of localization regulation of cellular process negative regulation of biological process negative regulation of transport negative regulation of cellular process regulation of intracellular transport negative regulation of intracellular transport regulation of biological process regulation of transport biological regulation regulation of vesicle-mediated transport vesicle-mediated transport between endosomal compartments regulation of early endosome to late endosome transport early endosome to late endosome transport regulation of cellular localization negative regulation of early endosome to late endosome transport regulation of neuron projection development multicellular organismal process regulation of cellular component organization positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization cellular response to stimulus regulation of signaling regulation of Wnt signaling pathway cell surface receptor signaling pathway signaling regulation of signal transduction cell communication regulation of response to stimulus regulation of cell communication signal transduction Wnt signaling pathway response to bacterium import into cell negative regulation of endocytosis negative regulation of phagocytosis phagocytosis regulation of endocytosis negative regulation of cellular component organization regulation of phagocytosis endocytosis negative regulation of protein transport regulation of protein localization regulation of establishment of protein localization negative regulation of establishment of protein localization regulation of protein transport negative regulation of protein localization catabolic process macromolecule catabolic process negative regulation of protein catabolic process regulation of primary metabolic process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process vesicle budding from membrane intralumenal vesicle formation vesicle organization organelle organization endosome organization endomembrane system organization 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 membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle protein-containing complex cellular anatomical structure membrane membrane protein complex retromer complex endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle clathrin-coated vesicle coated vesicle cytoplasm vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol early phagosome phagocytic vesicle endocytic vesicle early endosome endosome 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
A, B, C, D	IPR001683	Phox homology	Domain
A, B, C, D	IPR042137	Vertebrate SNX3, PX domain	Domain
A, B, C, D	IPR036871	PX domain superfamily	Homologous Superfamily
A, B, C, D	IPR051074	Sorting Nexin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O60493	microphthalmia acute myeloid leukemia medulloblastoma primitive neuroectodermal tumor intellectual disability large cell medulloblastoma 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.