1NUB | pdb_00001nub

HELIX C DELETION MUTANT OF BM-40 FS-EC DOMAIN PAIR

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)
A	d1nuba1	All alpha proteins	EF Hand-like	EF-hand	Osteonectin	C-terminal (EC) domain of BM-40/SPARC/osteonectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1nuba2	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	Follistatin (FS) module N-terminal domain, FS-N	Domain of BM-40/SPARC/osteonectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1nuba3	Small proteins	Kazal-type serine protease inhibitors	Kazal-type serine protease inhibitors	Ovomucoid domain III-like	Domain of BM-40/SPARC/osteonectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1nubb1	All alpha proteins	EF Hand-like	EF-hand	Osteonectin	C-terminal (EC) domain of BM-40/SPARC/osteonectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1nubb2	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	Follistatin (FS) module N-terminal domain, FS-N	Domain of BM-40/SPARC/osteonectin	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1nubb3	Small proteins	Kazal-type serine protease inhibitors	Kazal-type serine protease inhibitors	Ovomucoid domain III-like	Domain of BM-40/SPARC/osteonectin	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)
A	SCOP2 Family	Osteonectin	8024923	4000923	SCOP2 (2022-06-29)
A	SCOP2 Family	Follistatin (FS) module N-terminal domain, FS-N	8025973	4003221	SCOP2 (2022-06-29)
A	SCOP2 Family	Kazal-type serine protease inhibitors	8026324	4003413	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EF-hand	8037302	3001983	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EGF/Laminin-like	8038352	3000412	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Kazal-type serine protease inhibitors	8038703	3000605	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	EGF/Laminin-like	8038352	3000412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Kazal-type serine protease inhibitors	8038703	3000605	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EF-hand	8037302	3001983	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	Kazal_1	e1nubA2	A: few secondary structure elements	X: Kazal-type serine protease inhibitors-like	H: Kazal-type serine protease inhibitors	T: Kazal-type serine protease inhibitors	F: Kazal_1	ECOD (develop294)
A	EF-hand_5, EF-hand_6, EF-hand_7	e1nubA1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_5, EF-hand_6, EF-hand_7	ECOD (develop294)
A	Sushi	e1nubA3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Sushi	ECOD (develop294)
B	EF-hand_5, EF-hand_6, EF-hand_7	e1nubB1	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: EF-hand_5, EF-hand_6, EF-hand_7	ECOD (develop294)
B	Kazal_1	e1nubB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Kazal_1	ECOD (develop294)
B	Sushi	e1nubB3	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Sushi	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
A	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	3.30.60.30	Alpha Beta	2-Layer Sandwich	Wheat Germ Agglutinin (Isolectin 2)	domain 1	CATH (4.3.0)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09289	Follistatin/Osteonectin-like EGF domain (FOLN)	Follistatin/Osteonectin-like EGF domain	Members of this family are predominantly found in osteonectin and follistatin and adopt an EGF-like fold [1,2].	Domain
A, B	PF00050	Kazal-type serine protease inhibitor domain (Kazal_1)	Kazal-type serine protease inhibitor domain	Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containi ...	Usually indicative of serine protease inhibitors. However, kazal-like domains are also seen in the extracellular part of agrins, which are not known to be protease inhibitors. Kazal domains often occur in tandem arrays. Small alpha+beta fold containing three disulphides. Alignment also includes a single domain from transporters in the OATP/PGT family Swiss:P46721.	Domain
A, B	PF10591	Secreted protein acidic and rich in cysteine Ca binding region (SPARC_Ca_bdg)	Secreted protein acidic and rich in cysteine Ca binding region	The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each c ...	The SPARC_Ca_bdg domain of Secreted Protein Acidic and Rich in Cysteine is responsible for the anti-spreading activity of human urothelial cells. It is rich in alpha-helices. This extracellular calcium-binding domain contains two EF-hands that each coordinates one Ca2+ ion, forming a helix-loop-helix structure that not only drives the conformation of the protein but is also necessary for biological activity. The anti-spreading activity was dependent on the coordination of Ca2+ by a Glu residue at the Z position of EF-hand 2 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	BASEMENT MEMBRANE PROTEIN BM-40	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding extracellular matrix binding collagen binding protein-containing complex binding	positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration positive regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process endothelial cell migration biological regulation positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of endothelial cell migration positive regulation of cell motility regulation of cell migration regulation of endothelial cell migration cell migration cellular process cell motility locomotion positive regulation of cellular process developmental process anatomical structure morphogenesis regulation of developmental process anatomical structure development cell morphogenesis regulation of cell morphogenesis regulation of anatomical structure morphogenesis regulation of cellular component organization cellular component organization regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization cellular component organization or biogenesis regulation of biological quality ear morphogenesis embryonic organ morphogenesis multicellular organismal process ear development sensory organ development tube development semicircular canal morphogenesis animal organ development embryonic morphogenesis embryo development multicellular organism development tube morphogenesis semicircular canal development sensory organ morphogenesis inner ear development inner ear morphogenesis animal organ morphogenesis embryonic organ development negative regulation of biological process angiogenesis regulation of vasculature development regulation of multicellular organismal process system development blood vessel development regulation of multicellular organismal development blood vessel morphogenesis negative regulation of blood vessel morphogenesis negative regulation of developmental process negative regulation of angiogenesis vasculature development circulatory system development negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation negative regulation of endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation negative regulation of cellular process regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix basement membrane cell periphery membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle nuclear lumen nuclear matrix basement membrane cell periphery extracellular matrix external encapsulating structure cell surface plasma membrane membrane cytoplasm platelet alpha granule membrane intracellular vesicle endomembrane system cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle secretory granule secretory vesicle vesicle organelle membrane platelet alpha granule secretory granule membrane extracellular region vesicle lumen cytoplasmic vesicle lumen secretory granule lumen platelet alpha granule lumen endocytic vesicle lumen endocytic vesicle extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015369	Follistatin/Osteonectin EGF domain	Domain
A, B	IPR036058	Kazal domain superfamily	Homologous Superfamily
A, B	IPR002350	Kazal domain	Domain
A, B	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
A, B	IPR037641	SPARC, follistatin-like domain	Domain
A, B	IPR003645	Follistatin-like, N-terminal	Domain
A, B	IPR001999	Osteonectin-like, conserved site	Conserved Site
A, B	IPR019577	SPARC/Testican, calcium-binding domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P09486	osteogenesis imperfecta acute myeloid leukemia osteogenesis imperfecta type 17 plasma cell myeloma adrenal cortex carcinoma uremia Hyperalgesia colorectal cancer hepatitis osteogenesis imperfecta type 4 intervertebral disc degenerative disorder kidney disease cirrhosis of liver malignant colon neoplasm ovarian cancer osteogenesis imperfecta acute myeloid leukemia osteogenesis imperfecta type 17 plasma cell myeloma adrenal cortex carcinoma uremia Hyperalgesia colorectal cancer hepatitis osteogenesis imperfecta type 4 intervertebral disc degenerative disorder kidney disease cirrhosis of liver malignant colon neoplasm ovarian cancer thrombocytopenia malignant pancreatic neoplasm Emery-Dreifuss muscular dystrophy mucopolysaccharidosis type 4 nasopharyngeal carcinoma glioblastoma oligodendroglioma adrenal carcinoma ovarian neoplasm astrocytic tumor juvenile dermatomyositis pancreatic intraductal papillary-mucinous neoplasm Becker muscular dystrophy limb-girdle muscular dystrophy chronic kidney disease pterygium subependymal giant cell astrocytoma transitional cell carcinoma coronary artery disease malignant glioma Down syndrome esophageal adenocarcinoma myeloid neoplasm gastric cancer osteochondrodysplasia pancreatic ductal adenocarcinoma atopic eczema pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia benign colon neoplasm plasma cell neoplasm colorectal carcinoma ulcerative colitis cystic fibrosis Duchenne muscular dystrophy medulloblastoma exocrine pancreatic carcinoma myocardial ischemia gastric carcinoma hepatocellular carcinoma invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous carcinoma atypical teratoid rhabdoid tumor large cell medulloblastoma pilocytic astrocytoma breast cancer primitive neuroectodermal tumor Sjogren syndrome colonic neoplasm malignant ependymoma

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.