2QYP | pdb_00002qyp

Orthorhombic Crystal Structure of Human Saposin C Dimer in Open Conformation

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)
B	d2qypb2	All alpha proteins	Saposin-like	Saposin	NKL-like	Saposin C	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2qypb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2qypa_	All alpha proteins	Saposin-like	Saposin	NKL-like	Saposin C	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)
B	SCOP2B Superfamily	Saposin	8042048	3000601	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Saposin	8042048	3000601	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	SapB_2,SapB_1	e2qypB2	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: SapB_2,SapB_1	ECOD (v294.1)
A	Globin	e2qypA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: Globin	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.225.10	Mainly Alpha	Orthogonal Bundle	NK-Lysin	Saposin-like	CATH (4.3.0)
A	1.10.225.10	Mainly Alpha	Orthogonal Bundle	NK-Lysin	Saposin-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05184	Saposin-like type B, region 1 (SapB_1)	Saposin-like type B, region 1	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH sta ...	Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity [1,2]. It is one of the most studied members of the saposin protein family and it is involved in the hydrolysis of glycolipids and glycerolipids. SapB is unique in the saposin family in that it facilitates degradation by interacting with the substrate, not the enzymes [3].	Domain
A, B	PF03489	Saposin-like type B, region 2 (SapB_2)	Saposin-like type B, region 2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Proactivator polypeptide	protein binding binding enzyme binding protease binding ceramide binding organic acid binding sphingolipid binding glycolipid binding ganglioside GM3 binding glycosphingolipid binding ion binding ganglioside binding anion binding lipid binding protein binding binding enzyme binding protease binding ceramide binding organic acid binding sphingolipid binding glycolipid binding ganglioside GM3 binding glycosphingolipid binding ion binding ganglioside binding anion binding lipid binding carboxylic acid binding carbohydrate derivative binding monocarboxylic acid binding small molecule binding scaffold protein binding phospholipid binding ganglioside GM1 binding ganglioside GT1b binding enzyme regulator activity enzyme activator activity molecular function activator activity molecular function regulator activity identical protein binding protein homodimerization activity protein dimerization activity ganglioside GM2 binding ganglioside GP1c binding	developmental process epithelial cell differentiation involved in prostate gland development multicellular organismal process epithelium development reproductive system development cellular developmental process prostate gland development reproductive process gland development animal organ development urogenital system development tissue development developmental process involved in reproduction epithelial cell differentiation multicellular organism development developmental process epithelial cell differentiation involved in prostate gland development multicellular organismal process epithelium development reproductive system development cellular developmental process prostate gland development reproductive process gland development animal organ development urogenital system development tissue development developmental process involved in reproduction epithelial cell differentiation multicellular organism development cell differentiation anatomical structure development reproductive structure development cellular process system development regulation of biological process regulation of cellular process regulation of lipid metabolic process biological regulation primary metabolic process metabolic process regulation of metabolic process lipid metabolic process regulation of primary metabolic process sphingolipid metabolic process biosynthetic process macromolecule metabolic process gene expression macromolecule biosynthetic process cellular localization organic anion transport nitrogen compound transport carboxylic acid transport transport glycolipid transport lipid localization lipid transport localization within membrane carbohydrate derivative transport establishment of localization organic acid transport localization ceramide transport macromolecule localization ganglioside GM1 transport to membrane establishment of localization in cell vacuolar transport intracellular transport lysosomal transport cellular response to stimulus response to stimulus signaling cell communication adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway adenylate cyclase-modulating G protein-coupled receptor signaling pathway G protein-coupled receptor signaling pathway signal transduction catabolic process autophagy regulation of catabolic process regulation of autophagy process utilizing autophagic mechanism developmental growth growth organ growth prostate gland growth	membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle intracellular vesicle endomembrane system bounding membrane of organelle vesicle membrane cytoplasmic vesicle vacuolar membrane membrane azurophil granule lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane organelle membrane secretory granule membrane cell periphery plasma membrane endosome late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011001	Saposin-like	Homologous Superfamily
A, B	IPR008373	Saposin	Family
A, B	IPR007856	Saposin-like type B, region 1	Domain
A, B	IPR021165	Saposin, chordata	Family
A, B	IPR003119	Saposin A-type domain	Domain
A, B	IPR008139	Saposin B type domain	Domain
A, B	IPR051428	Sphingolipid Activators and Surfactant Proteins	Family
A, B	IPR008138	Saposin B type, region 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P07602	Krabbe disease, atypical, due to saposin A deficiency atypical Gaucher disease due to saposin C deficiency encephalopathy due to prosaposin deficiency metachromatic leukodystrophy due to saposin b deficiency metachromatic leukodystrophy leukodystrophy gangliosidosis Gaucher disease myopathy Parkinson disease sphingolipidosis astrocytic tumor brain disease inborn errors of metabolism Metachromatic Leukodystrophy, Infant Krabbe disease, atypical, due to saposin A deficiency atypical Gaucher disease due to saposin C deficiency encephalopathy due to prosaposin deficiency metachromatic leukodystrophy due to saposin b deficiency metachromatic leukodystrophy leukodystrophy gangliosidosis Gaucher disease myopathy Parkinson disease sphingolipidosis astrocytic tumor brain disease inborn errors of metabolism Metachromatic Leukodystrophy, Infant neurodegenerative disease plasma cell myeloma ovarian cancer psoriasis B-cell chronic lymphocytic leukemia IgA glomerulonephritis intellectual disability lysosomal storage disease

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.