4DUR

The X-ray Crystal Structure of Full-Length type II Human Plasminogen

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Trypsin-like serine proteases	8042267	3000114	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Kringle-like	8038646	3000761	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Kringle-like	8038646	3000761	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trypsin-like serine proteases	8042267	3000114	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	Trypsin_1	e4durA4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
A	Kringle	e4durA1	A: few secondary structure elements	X: Kringle-like (From Topology)	H: Kringle-like (From Topology)	T: Kringle-like	F: Kringle	ECOD (1.6)
A	PAN_1	e4durA6	A: few secondary structure elements	X: Hairpin loop containing domain-like (From Topology)	H: Hairpin loop containing domain-like (From Topology)	T: Hairpin loop containing domain-like	F: PAN_1	ECOD (1.6)
B	Trypsin_1	e4durB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel 2	F: Trypsin_1	ECOD (1.6)
B	Kringle	e4durB6	A: few secondary structure elements	X: Kringle-like (From Topology)	H: Kringle-like (From Topology)	T: Kringle-like	F: Kringle	ECOD (1.6)
B	PAN_1	e4durB7	A: few secondary structure elements	X: Hairpin loop containing domain-like (From Topology)	H: Hairpin loop containing domain-like (From Topology)	T: Hairpin loop containing domain-like	F: PAN_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	CATH (4.3.0)
A	2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	CATH (4.3.0)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B	3.50.4.10	Alpha Beta	3-Layer(bba) Sandwich	Hepatocyte Growth Factor	Hepatocyte Growth Factor	CATH (4.3.0)
B	2.40.20.10	Mainly Beta	Beta Barrel	Plasminogen Kringle 4	Plasminogen Kringle 4	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00051	Kringle domain (Kringle)	Kringle domain	Kringle domains have been found in plasminogen, hepatocyte growth factors, prothrombin, and apolipoprotein A. Structure is disulfide-rich, nearly all-beta.	Domain
A, B	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain
A, B	PF00024	PAN domain (PAN_1)	PAN domain	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some the ...	The PAN domain [1] contains a conserved core of three disulphide bridges. In some members of the family there is an additional fourth disulphide bridge the links the N and C termini of the domain. The domain is found in diverse proteins, in some they mediate protein-protein interactions, in others they mediate protein-carbohydrate interactions.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Plasminogen	protein antigen binding protein binding binding antigen 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 protein-folding chaperone binding protein domain specific binding protein antigen binding protein binding binding antigen 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 protein-folding chaperone binding protein domain specific binding signaling receptor binding apolipoprotein binding enzyme binding protease binding kinase binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process regulation of cell adhesion multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding regulation of biological process regulation of cellular process regulation of cell adhesion negative regulation of biological process negative regulation of cell adhesion cell adhesion cell-cell adhesion negative regulation of cell-cell adhesion mediated by cadherin cell-cell adhesion mediated by cadherin negative regulation of cell-cell adhesion negative regulation of cellular process regulation of cell-cell adhesion cellular process regulation of cell-cell adhesion mediated by cadherin developmental process muscle structure development cellular developmental process cell differentiation anatomical structure development myoblast differentiation regulation of response to external stimulus regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding negative regulation of hemostasis fibrinolysis 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 leukocyte migration immune system process mononuclear cell migration cell migration cell motility tissue regeneration developmental growth growth regeneration trans-synaptic signaling regulation of signaling signaling trans-synaptic signaling, modulating synaptic transmission modulation of chemical synaptic transmission cell-cell signaling cell communication chemical synaptic transmission trans-synaptic signaling by BDNF, modulating synaptic transmission synaptic signaling regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication trans-synaptic signaling by BDNF cellular homeostasis homeostatic process muscle cell cellular homeostasis labyrinthine layer blood vessel development placenta blood vessel development placenta development chordate embryonic development animal organ development labyrinthine layer development embryo development in utero embryonic development vasculature development circulatory system development multicellular organism development embryonic placenta development embryo development ending in birth or egg hatching embryonic organ development blood vessel development system development tissue remodeling cellular component organization cellular component disassembly extracellular matrix disassembly extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction cell differentiation involved in embryonic placenta development reproductive process developmental process involved in reproduction trophoblast giant cell differentiation 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 regulation of fibrinolysis positive regulation of multicellular organismal process negative regulation of fibrinolysis positive regulation of locomotion regulation of cell motility regulation of blood vessel endothelial cell migration endothelial cell migration positive regulation of cell migration positive regulation of epithelial cell migration tissue migration ameboidal-type cell migration positive regulation of cell motility regulation of cell migration blood vessel endothelial cell migration regulation of endothelial cell migration epithelial cell migration regulation of epithelial cell migration locomotion positive regulation of cellular process positive regulation of blood vessel endothelial cell migration epithelium migration regulation of locomotion positive regulation of endothelial cell migration negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation regulation of cell-substrate adhesion cell-substrate adhesion negative regulation of cell-substrate adhesion positive regulation of fibrinolysis organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure collagen-containing extracellular matrix synapse cell junction glutamatergic synapse 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 cytoplasmic vesicle organelle lumen secretory granule secretory vesicle cytoplasm platelet alpha granule platelet alpha granule lumen blood microparticle Schaffer collateral - CA1 synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, B	IPR001254	Serine proteases, trypsin domain	Domain
A, B	IPR000001	Kringle	Domain
A, B	IPR018056	Kringle, conserved site	Conserved Site
A, B	IPR003609	PAN/Apple domain	Domain
A, B	IPR013806	Kringle-like fold	Homologous Superfamily
A, B	IPR038178	Kringle superfamily	Homologous Superfamily
A, B	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B	IPR023317	Peptidase S1A, plasmin	Family
A, B	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P00747	thrombophilia hypertensive disorder hypoplasminogenemia heart disease Venous Thrombosis ligneous conjunctivitis pulmonary embolism temporal arteritis inborn carbohydrate metabolic disorder abdominal aortic aneurysm leukocyte disease aortic stenosis major depressive disorder cerebrovascular disorder myocardial infarction thrombophilia hypertensive disorder hypoplasminogenemia heart disease Venous Thrombosis ligneous conjunctivitis pulmonary embolism temporal arteritis inborn carbohydrate metabolic disorder abdominal aortic aneurysm leukocyte disease aortic stenosis major depressive disorder cerebrovascular disorder myocardial infarction peripheral arterial disease schizophrenia endometriosis acute kidney failure acute myocardial infarction atherosclerosis nephrosclerosis coronary artery disease drug-induced liver injury thrombotic disease hydrocephalus cancer metabolic syndrome X pancreatic ductal adenocarcinoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.