2KRI | pdb_00002kri

Structure of a complex between domain V of beta2-glycoprotein I and the fourth ligand-binding module from LDLR determined with Haddock

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	d2kria_	Small proteins	Complement control module/SCR domain	Complement control module/SCR domain	Complement control module/SCR domain	beta2-glycoprotein I	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2krib_	Small proteins	LDL receptor-like module	LDL receptor-like module	LDL receptor-like module	Ligand-binding domain of low-density lipoprotein receptor	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	SCOP2B Superfamily	Sushi/CCP/SCR domain	8038859	3000902	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	Pyrophosphatase	e2kriA1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: sensor domains	T: sensor domains	F: Pyrophosphatase	ECOD (develop294)
B	RVP	e2kriB1	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: RVP	ECOD (develop294)

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
B	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Beta-2-glycoprotein 1	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 protein binding enzyme binding lipase binding heparin binding glycosaminoglycan 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 protein binding enzyme binding lipase binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding identical protein binding	plasma lipoprotein particle organization multicellular organismal process regulation of biological process protein-containing complex organization protein-containing complex remodeling protein-lipid complex organization biological regulation plasma lipoprotein particle remodeling regulation of plasma lipoprotein particle levels cellular component organization chylomicron remodeling triglyceride-rich lipoprotein particle remodeling protein-lipid complex remodeling cellular process plasma lipoprotein particle organization multicellular organismal process regulation of biological process protein-containing complex organization protein-containing complex remodeling protein-lipid complex organization biological regulation plasma lipoprotein particle remodeling regulation of plasma lipoprotein particle levels cellular component organization chylomicron remodeling triglyceride-rich lipoprotein particle remodeling protein-lipid complex remodeling cellular process cellular component organization or biogenesis 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 negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation 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 very-low-density lipoprotein particle remodeling zymogen activation primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process plasminogen activation 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 regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process regulation of lipid metabolic process regulation of primary metabolic process positive regulation of metabolic process triglyceride metabolic process positive regulation of lipid metabolic process glycerolipid metabolic process acylglycerol metabolic process regulation of metabolic process positive regulation of cellular 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 intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure platelet dense granule lumen cytoplasmic vesicle membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure 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 surface chylomicron very-low-density lipoprotein particle triglyceride-rich plasma lipoprotein particle
B	Low-density lipoprotein receptor	amyloid-beta binding binding peptide binding molecular adaptor activity identical protein binding protein binding virus receptor activity exogenous protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding lipoprotein particle receptor activity amyloid-beta binding binding peptide binding molecular adaptor activity identical protein binding protein binding virus receptor activity exogenous protein binding cation binding ion binding calcium ion binding metal ion binding small molecule binding lipoprotein particle receptor activity cargo receptor activity very-low-density lipoprotein particle receptor activity enzyme binding protease binding clathrin heavy chain binding clathrin binding low-density lipoprotein particle receptor activity lipoprotein particle binding protein-containing complex binding protein-lipid complex binding low-density lipoprotein particle binding	multicellular organismal process catabolic process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic process metabolic process cellular process amyloid-beta clearance regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process multicellular organismal process catabolic process amyloid-beta metabolic process amyloid-beta clearance by cellular catabolic process metabolic process cellular process amyloid-beta clearance regulation of defense response regulation of biological process response to stimulus regulation of response to external stimulus defense response biological regulation positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress response to stress positive regulation of defense response inflammatory response localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport regulation of biosynthetic process regulation of cellular process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process macromolecule localization phospholipid transport lipid localization lipid transport organophosphate ester transport cholesterol transport sterol transport organic hydroxy compound transport plasma lipoprotein particle clearance regulation of plasma lipoprotein particle levels developmental process blood vessel morphogenesis tube development artery development vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development artery morphogenesis blood vessel development system development regulation of cholesterol metabolic process sterol metabolic process steroid metabolic process regulation of steroid metabolic process regulation of lipid metabolic process cholesterol metabolic process alcohol metabolic process primary metabolic process regulation of primary metabolic process secondary alcohol metabolic process regulation of small molecule metabolic process small molecule metabolic process lipid metabolic process response to nutrient levels response to caloric restriction regulation of protein metabolic process negative regulation of metabolic process negative regulation of biological process negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of low-density lipoprotein particle clearance negative regulation of low-density lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance regulation of multicellular organismal process low-density lipoprotein particle clearance negative regulation of multicellular organismal process intestinal lipid absorption digestion system process intestinal absorption digestive system process intestinal cholesterol absorption lipid digestion cellular response to stimulus cellular response to low-density lipoprotein particle stimulus response to endogenous stimulus response to chemical response to lipoprotein particle cellular response to lipoprotein particle stimulus cellular localization intracellular lipid transport intracellular cholesterol transport intracellular transport intracellular sterol transport establishment of localization in cell receptor-mediated endocytosis involved in cholesterol transport receptor-mediated endocytosis cholesterol import diterpenoid metabolic process retinoid metabolic process terpenoid metabolic process isoprenoid metabolic process astrocyte differentiation negative regulation of astrocyte activation regulation of cell activation regulation of neurogenesis regulation of cell differentiation astrocyte activation glial cell development regulation of astrocyte differentiation regulation of cell development gliogenesis cell differentiation nervous system development negative regulation of gliogenesis negative regulation of glial cell differentiation central nervous system development negative regulation of response to external stimulus negative regulation of defense response glial cell activation neuroinflammatory response cellular developmental process regulation of developmental process negative regulation of inflammatory response cell development regulation of gliogenesis regulation of nervous system development neurogenesis negative regulation of neurogenesis astrocyte development regulation of neuroinflammatory response negative regulation of nervous system development negative regulation of cell differentiation regulation of multicellular organismal development negative regulation of response to stimulus negative regulation of developmental process cell activation regulation of glial cell differentiation negative regulation of astrocyte differentiation negative regulation of cell activation negative regulation of cell development glial cell differentiation regulation of astrocyte activation negative regulation of neuroinflammatory response regulation of macrophage activation regulation of leukocyte activation myeloid leukocyte activation leukocyte activation macrophage activation leukocyte activation involved in inflammatory response regulation of immune system process negative regulation of microglial cell activation negative regulation of immune system process immune system process microglial cell activation regulation of microglial cell activation negative regulation of leukocyte activation negative regulation of macrophage activation sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis neutral lipid metabolic process neutral lipid biosynthetic process regulation of triglyceride metabolic process positive regulation of triglyceride metabolic process lipid biosynthetic process acylglycerol biosynthetic process triglyceride metabolic process triglyceride biosynthetic process positive regulation of lipid metabolic process regulation of triglyceride biosynthetic process positive regulation of triglyceride biosynthetic process glycerolipid biosynthetic process positive regulation of lipid biosynthetic process glycerolipid metabolic process regulation of lipid biosynthetic process acylglycerol metabolic process behavior learning or memory long-term memory nervous system process cognition memory high-density lipoprotein particle clearance regulation of protein catabolic process in the vacuole positive regulation of protein metabolic process lysosomal protein catabolic process macromolecule catabolic process positive regulation of lysosomal protein catabolic process protein catabolic process in the vacuole protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of lysosomal protein catabolic process positive regulation of protein catabolic process in the vacuole regulation of protein catabolic process regulation of signaling negative regulation of signaling signaling regulation of receptor recycling negative regulation of receptor recycling receptor recycling receptor metabolic process response to lipid response to fatty acid response to oxygen-containing compound cellular response to oxygen-containing compound cellular response to fatty acid cellular response to chemical stimulus cellular response to lipid lipoprotein metabolic process lipoprotein catabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of cellular component organization negative regulation of amyloid fibril formation regulation of amyloid fibril formation amyloid fibril formation cellular component organization negative regulation of supramolecular fiber organization cellular component organization or biogenesis negative regulation of cellular component organization regulation of supramolecular fiber organization supramolecular fiber organization phospholipid catabolic process glycerophospholipid metabolic process glycerolipid catabolic process organophosphate catabolic process phospholipid metabolic process phosphate-containing compound metabolic process phosphatidylcholine metabolic process phosphorus metabolic process regulation of phospholipid catabolic process lipid catabolic process regulation of phosphatidylcholine metabolic process regulation of phospholipid metabolic process regulation of lipid catabolic process phosphatidylcholine catabolic process organophosphate metabolic process regulation of phosphatidylcholine catabolic process regulation of phosphorus metabolic process glycerophospholipid catabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane basal part of cell basal plasma membrane plasma membrane region basolateral plasma membrane protein-containing complex receptor complex Golgi apparatus endosome membrane endosome sorting endosome somatodendritic compartment endolysosome membrane lytic vacuole endolysosome lysosome vacuolar membrane vacuole lytic vacuole membrane lysosomal membrane early endosome PCSK9-LDLR complex low-density lipoprotein particle extracellular region plasma lipoprotein particle extracellular space lipoprotein particle protein-lipid complex late endosome

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	IPR015104	Beta-2-glycoprotein-1 fifth domain	Domain
B	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
B	IPR000033	LDLR class B repeat	Repeat
B	IPR001881	EGF-like calcium-binding domain	Domain
B	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
B	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
B	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
B	IPR000742	EGF-like domain	Domain
B	IPR051221	Low-density lipoprotein receptor-related	Family
B	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

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
B	Pharos: P01130	familial hypercholesterolemia Dyslipidemias abdominal aortic aneurysm non-alcoholic fatty liver disease coronary artery disease obesity disorder Q fever amyotrophic lateral sclerosis type 1 hyperplasia atherosclerosis ovarian cancer psoriasis sinusitis glioblastoma invasive ductal breast carcinoma familial hypercholesterolemia Dyslipidemias abdominal aortic aneurysm non-alcoholic fatty liver disease coronary artery disease obesity disorder Q fever amyotrophic lateral sclerosis type 1 hyperplasia atherosclerosis ovarian cancer psoriasis sinusitis glioblastoma invasive ductal breast carcinoma arteriosclerosis disorder lung adenocarcinoma atypical teratoid rhabdoid tumor malignant pancreatic neoplasm cystic fibrosis pancreatic ductal adenocarcinoma fatty liver disease Sjogren syndrome heart disease type 2 diabetes mellitus lung cancer breast cancer medulloblastoma congestive heart failure non-small cell lung carcinoma osteosarcoma ductal breast carcinoma in situ peripheral arterial disease exocrine pancreatic carcinoma familial hyperlipidemia sarcoidosis Gaucher disease spina bifida hydrolethalus syndrome ulcerative colitis hyperlipidemia alcohol abuse lung carcinoma carotid artery disease myocardial infarction

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.