1NZI | pdb_00001nzi

Crystal Structure of the CUB1-EGF Interaction Domain of Complement Protease C1s

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	d1nzib1	All beta proteins	CUB-like	Spermadhesin, CUB domain	Spermadhesin, CUB domain	Complement C1S component	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1nzib2	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Complement C1S component	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1nzia1	All beta proteins	CUB-like	Spermadhesin, CUB domain	Spermadhesin, CUB domain	Complement C1S component	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1nzia2	Small proteins	Knottins (small inhibitors, toxins, lectins)	EGF/Laminin	EGF-type module	Complement C1S component	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	Spermadhesin, CUB domain	8033760	3001412	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	EGF/Laminin-like	8033759	3000412	SCOP2B (2022-06-29)
A	SCOP2 Family	EGF-type module	8021379	4003198	SCOP2 (2022-06-29)
A	SCOP2 Family	spermadhesin, cub domain	8021380	4002562	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	EGF/Laminin-like	8033759	3000412	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Spermadhesin, CUB domain	8033760	3001412	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)
B	TPK_B1_binding	e1nziB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: TPK_B1_binding	ECOD (v294.1)
B	Sushi	e1nziB2	A: a/b three-layered sandwiches	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Sushi	ECOD (v294.1)
A	CUB	e1nziA1	A: beta sandwiches	X: jelly-roll	H: Spermadhesin, CUB domain	T: Spermadhesin, CUB domain	F: CUB	ECOD (v294.1)
A	FXa_inhibition	e1nziA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: FXa_inhibition	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
B	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)
A	2.60.120.290	Mainly Beta	Sandwich	Jelly Rolls	Spermadhesin, CUB domain	CATH (4.3.0)
A	2.10.25.10	Mainly Beta	Ribbon	Laminin	Laminin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
A, B	PF00431	CUB domain (CUB)	CUB domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Complement C1s component	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity identical protein binding protein binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to other organism response to stress innate immune response response to external biotic stimulus proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	protein-containing complex cellular anatomical structure complement component C1 complex extracellular region extracellular protein-containing complex cell surface other organism part symbiont cell surface blood microparticle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A, B	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A, B	IPR000436	Sushi/SCR/CCP domain	Domain
A, B	IPR000859	CUB domain	Domain
A, B	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, B	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, B	IPR001254	Serine proteases, trypsin domain	Domain
A, B	IPR001881	EGF-like calcium-binding domain	Domain
A, B	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A, B	IPR024175	Peptidase S1A, complement C1r/C1S/mannan-binding	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P09871	complement component C1s deficiency Ehlers-Danlos syndrome Hashimoto thyroiditis autoimmune hepatitis autoimmune disease Ehlers-Danlos syndrome, periodontal type 2 Hereditary Angioedema Types I and II subependymal giant cell astrocytoma esophageal adenocarcinoma hereditary angioedema type 2 invasive ductal breast carcinoma adrenal cortex carcinoma limb-girdle muscular dystrophy malignant colon neoplasm chronic kidney disease complement component C1s deficiency Ehlers-Danlos syndrome Hashimoto thyroiditis autoimmune hepatitis autoimmune disease Ehlers-Danlos syndrome, periodontal type 2 Hereditary Angioedema Types I and II subependymal giant cell astrocytoma esophageal adenocarcinoma hereditary angioedema type 2 invasive ductal breast carcinoma adrenal cortex carcinoma limb-girdle muscular dystrophy malignant colon neoplasm chronic kidney disease malignant mesothelioma myopathy pancreatic ductal adenocarcinoma diabetes mellitus pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Ehlers-Danlos syndrome, periodontal type 1 psoriasis ulcerative colitis gastric carcinoma head and neck cancer juvenile dermatomyositis angioedema lung cancer malignant ependymoma malignant pancreatic neoplasm chronic obstructive pulmonary disease non-small cell lung carcinoma cystic fibrosis pancreatic intraductal papillary-mucinous carcinoma Duchenne muscular dystrophy pilocytic astrocytoma Sjogren syndrome Emery-Dreifuss muscular dystrophy glioblastoma heart disease large cell medulloblastoma atopic eczema lung carcinoma Becker muscular dystrophy malignant glioma medulloblastoma ovarian cancer dermatomyositis pancreatic intraductal papillary-mucinous neoplasm pituitary 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.