1QUB

CRYSTAL STRUCTURE OF THE GLYCOSYLATED FIVE-DOMAIN HUMAN BETA2-GLYCOPROTEIN I PURIFIED FROM BLOOD PLASMA

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	d1quba1	Small proteins	Complement control module/SCR domain	Complement control module/SCR domain	Complement control module/SCR domain	beta2-glycoprotein I	(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	Sushi/CCP/SCR domain	8026473	4003458	SCOP2 (2022-06-29)
A	SCOP2 Family	Sushi/CCP/SCR domain	8026475	4003458	SCOP2 (2022-06-29)
A	SCOP2 Family	Sushi/CCP/SCR domain	8026477	4003458	SCOP2 (2022-06-29)
A	SCOP2 Family	Sushi/CCP/SCR domain	8026479	4003458	SCOP2 (2022-06-29)
A	SCOP2 Family	Sushi/CCP/SCR domain	8026480	4003458	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sushi/CCP/SCR domain	8038852	3000902	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sushi/CCP/SCR domain	8038854	3000902	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sushi/CCP/SCR domain	8038856	3000902	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sushi/CCP/SCR domain	8038858	3000902	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sushi/CCP/SCR domain	8038859	3000902	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)
A	Sushi_4	e1qubA1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_4	ECOD (1.6)
A	Sushi_2	e1qubA4	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_2	ECOD (1.6)
A	Sushi	e1qubA3	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi	ECOD (1.6)
A	Sushi_1	e1qubA2	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: Complement control module/SCR domain	F: Sushi_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF09014	Beta-2-glycoprotein-1 fifth domain (Sushi_2)	Beta-2-glycoprotein-1 fifth domain	The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively char ...	The fifth domain of beta-2-glycoprotein-1 (b2GP-1) is composed of four well-defined anti-parallel beta-strands and two short alpha-helices, as well as a long highly flexible loop. It plays an important role in the binding of b2GP-1 to negatively charged compounds and subsequent capture for binding of anti-b2GP-1 antibodies [1].	Domain
A	PF00084	Sushi repeat (SCR repeat) (Sushi)	Sushi repeat (SCR repeat)	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN (human beta2-Glycoprotein I)	enzyme regulator activity enzyme activator activity molecular function activator activity lipoprotein lipase activator activity molecular function regulator activity lipase activator activity binding phospholipid binding lipid binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding enzyme regulator activity enzyme activator activity molecular function activator activity lipoprotein lipase activator activity molecular function regulator activity lipase activator activity binding phospholipid binding lipid binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding protein binding	multicellular organismal process regulation of body fluid levels response to stimulus regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation response to stress regulation of response to stress coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis multicellular organismal process regulation of body fluid levels response to stimulus regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation response to stress regulation of response to stress coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis wound healing regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation biological regulation hemostasis response to external stimulus negative regulation of response to wounding blood coagulation negative regulation of hemostasis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process zymogen activation cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process plasminogen activation regulation of catalytic activity positive regulation of catalytic activity positive regulation of lipoprotein lipase activity regulation of lipoprotein lipase activity positive regulation of lipase activity positive regulation of triglyceride lipase activity regulation of molecular function positive regulation of molecular function positive regulation of hydrolase activity regulation of hydrolase activity regulation of lipase activity positive regulation of coagulation positive regulation of biological process positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing fibrinolysis regulation of fibrinolysis positive regulation of multicellular organismal process negative regulation of fibrinolysis myeloid cell apoptotic process regulation of cellular process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process negative regulation of myeloid cell apoptotic process apoptotic process regulation of myeloid cell apoptotic process programmed cell death negative regulation of locomotion regulation of cell motility endothelial cell migration negative regulation of endothelial cell migration regulation of locomotion regulation of cell migration regulation of endothelial cell migration negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration neutral lipid metabolic process triglyceride metabolic process cellular lipid metabolic process glycerolipid metabolic process acylglycerol metabolic process lipid metabolic process blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation protein activation cascade regulation of developmental process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis anatomical structure development regulation of anatomical structure morphogenesis system development blood vessel development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development 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 anatomical structure morphogenesis regulation of angiogenesis anatomical structure formation involved in morphogenesis 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 regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation localization transport macromolecule localization lipid localization lipid transport acylglycerol transport triglyceride transport establishment of localization muscle cell apoptotic process smooth muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of smooth muscle cell apoptotic process negative regulation of smooth muscle cell apoptotic process negative regulation of muscle cell apoptotic process	membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen cellular anatomical entity intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle platelet dense granule lumen cytoplasmic vesicle membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen cellular anatomical entity intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle platelet dense granule lumen cytoplasmic vesicle organelle lumen platelet dense granule organelle secretory granule secretory vesicle cytoplasm vesicle protein-containing complex extracellular region plasma lipoprotein particle high-density lipoprotein particle extracellular space lipoprotein particle protein-lipid complex extracellular exosome extracellular vesicle extracellular organelle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cell surface chylomicron very-low-density lipoprotein particle triglyceride-rich plasma lipoprotein particle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000436	Sushi/SCR/CCP domain	Domain
A	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily
A	IPR050350	Complement & Cell Adhesion Regulators	Family
A	IPR015104	Beta-2-glycoprotein-1 fifth domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P02749	antiphospholipid syndrome dilated cardiomyopathy drug-induced liver injury lung cancer malignant pancreatic neoplasm pancreatic intraductal papillary-mucinous neoplasm thrombophilia Chemical and Drug Induced Liver Injury lupus erythematosus non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia thrombotic disease malignant ependymoma pancreatic intraductal papillary-mucinous carcinoma schizophrenia

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.