6GWP

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6gwpa_	Multi-domain proteins (alpha and beta)	Serpins	Serpins	Serpins	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d6gwpb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
C	d6gwpc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Serpins	8041305	3001563	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	Serpin	e6gwpA1	A: a+b complex topology	X: Serpins (From Topology)	H: Serpins (From Topology)	T: Serpins	F: Serpin	ECOD (1.6)
B	V-set_8	e6gwpB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	V-set_8	e6gwpC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.497.10	Alpha Beta	2-Layer Sandwich	Antithrombin	Chain I, domain 2	CATH (utative)
A	2.30.39.10	Mainly Beta	Roll	Alpha-1-antitrypsin	domain 1	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B	VHH 2g-42, anti-PAI-1	VH	Vicugna pacos (alpaca)	IGHV3-301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202415-0)
C	VHH 2w-64, anti-PAI-1	VH	Vicugna pacos (alpaca)	IGHV3-301, IGHJ401	V-DOMAIN VH	IG	VH	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Heavy Chain	IGHV1	-	plasminogen activator inhibitor-1	SAbDab (2024-04-19)
C	Heavy Chain	IGHV1	-	plasminogen activator inhibitor-1	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00079	Serpin (serine protease inhibitor) (Serpin)	Serpin (serine protease inhibitor)	Structure is a multi-domain fold containing a bundle of helices and a beta sandwich.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Plasminogen Activator Inhibitor-1	protein binding binding signaling receptor binding enzyme binding protease binding enzyme regulator activity molecular function inhibitor activity peptidase regulator activity serine-type endopeptidase inhibitor activity molecular function regulator activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity	negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process regulation of smooth muscle cell migration biological regulation negative regulation of biological process smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process negative regulation of cell motility negative regulation of locomotion regulation of biological process regulation of cell motility regulation of cellular process regulation of smooth muscle cell migration biological regulation negative regulation of biological process smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process negative regulation of cell motility cell migration cellular process cell motility locomotion negative regulation of cell migration regulation of defense response response to stimulus regulation of response to external stimulus defense response 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 developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development cellular response to stimulus extrinsic apoptotic signaling pathway via death domain receptors signaling negative regulation of signaling regulation of signal transduction regulation of programmed cell death extrinsic apoptotic signaling pathway negative regulation of cell communication cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway signal transduction regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of extrinsic apoptotic signaling pathway via death domain receptors cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of extrinsic apoptotic signaling pathway via death domain receptors regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway regulation of body fluid levels regulation of response to wounding regulation of coagulation coagulation regulation of multicellular organismal process regulation of biological quality response to wounding regulation of hemostasis wound healing negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation hemostasis negative regulation of response to wounding blood coagulation negative regulation of hemostasis fibrinolysis negative regulation of coagulation negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process negative regulation of cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion negative regulation of cell adhesion cell adhesion cell adhesion mediated by integrin replicative senescence cellular metabolic process metabolic process response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin positive regulation of interleukin-8 production cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process cytokine production organic substance biosynthetic process regulation of cytokine production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular metabolic process interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process positive regulation of cellular biosynthetic process regulation of interleukin-8 production odontogenesis of dentin-containing tooth dentinogenesis odontogenesis animal organ development animal organ morphogenesis negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of catalytic activity negative regulation of endopeptidase activity regulation of primary metabolic process negative regulation of peptidase activity regulation of proteolysis proteolysis regulation of endopeptidase activity protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process organonitrogen compound metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of peptidase activity negative regulation of molecular function primary metabolic process regulation of molecular function regulation of hydrolase activity positive regulation of coagulation positive regulation of blood coagulation positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing regulation of fibrinolysis negative regulation of fibrinolysis regulation of developmental process regulation of vasculature development vascular wound healing regulation of anatomical structure morphogenesis regulation of multicellular organismal development negative regulation of blood vessel morphogenesis negative regulation of developmental process angiogenesis involved in wound healing negative regulation of angiogenesis negative regulation of vasculature development regulation of angiogenesis negative regulation of vascular wound healing regulation of vascular wound healing positive regulation of odontoblast differentiation cellular developmental process regulation of cell differentiation epithelial cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation cell differentiation neuroepithelial cell differentiation odontoblast differentiation epithelium development regulation of odontoblast differentiation tissue development positive regulation of epithelial cell differentiation columnar/cuboidal epithelial cell differentiation positive regulation of neuroepithelial cell differentiation regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis positive regulation of angiogenesis positive regulation of vasculature development positive regulation of monocyte chemotaxis positive regulation of locomotion positive regulation of chemotaxis positive regulation of cell migration regulation of monocyte chemotaxis taxis positive regulation of cell motility myeloid leukocyte migration positive regulation of mononuclear cell migration regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of leukocyte chemotaxis regulation of chemotaxis monocyte chemotaxis leukocyte migration immune system process mononuclear cell migration leukocyte chemotaxis regulation of protein maturation negative regulation of plasminogen activation negative regulation of cellular metabolic process protein maturation plasminogen activation zymogen activation negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing negative regulation of protein maturation regulation of plasminogen activation negative regulation of biosynthetic process negative regulation of protein processing defense response to Gram-negative bacterium defense response to bacterium defense response to other organism regulation of signaling receptor activity negative regulation of endothelial cell apoptotic process regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process regulation of cell-substrate adhesion cell-substrate adhesion negative regulation of smooth muscle cell-matrix adhesion negative regulation of cell-matrix adhesion regulation of smooth muscle cell-matrix adhesion smooth muscle cell-matrix adhesion cell-matrix adhesion regulation of cell-matrix adhesion negative regulation of cell-substrate adhesion regulation of leukotriene production involved in inflammatory response arachidonic acid metabolite production involved in inflammatory response production of molecular mediator involved in inflammatory response positive regulation of leukotriene production involved in inflammatory response leukotriene production involved in inflammatory response	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix plasma membrane membrane protein-containing complex peptidase inhibitor complex serine protease inhibitor complex protease inhibitor complex 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
B	VHH-2g-42	-	-	-
C	VHH-2w-64	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR023795	Serpin, conserved site	Conserved Site
A	IPR000215	Serpin family	Family
A	IPR036186	Serpin superfamily	Homologous Superfamily
A	IPR023796	Serpin domain	Domain
A	IPR042178	Serpin superfamily, domain 1	Homologous Superfamily
A	IPR042185	Serpin superfamily, domain 2	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P05121	atherosclerosis congestive heart failure nephrotic syndrome obesity disorder hypertensive disorder chronic kidney disease congenital plasminogen activator inhibitor type 1 deficiency Diabetes Mellitus, Experimental focal segmental glomerulosclerosis prostate cancer Behcet disease cholestasis nervous system disorder preeclampsia liver cancer atherosclerosis congestive heart failure nephrotic syndrome obesity disorder hypertensive disorder chronic kidney disease congenital plasminogen activator inhibitor type 1 deficiency Diabetes Mellitus, Experimental focal segmental glomerulosclerosis prostate cancer Behcet disease cholestasis nervous system disorder preeclampsia liver cancer thrombotic disease type 2 diabetes mellitus major depressive disorder ureteral obstruction malignant mesothelioma gastric neoplasm ovarian cancer pancreatic intraductal papillary-mucinous neoplasm heart failure atypical teratoid rhabdoid tumor inborn carbohydrate metabolic disorder kidney disease thrombophilia liver disease cystic fibrosis lung carcinoma ulcerative colitis diabetic kidney disease malignant ependymoma fatty liver disease gastric cancer arteriosclerosis disorder glioblastoma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atopic eczema autism cancer interstitial cystitis coronary artery disease liver neoplasm tuberculosis lung disease malignant glioma esophageal adenocarcinoma malignant pancreatic neoplasm gastric carcinoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma pilocytic astrocytoma attention deficit hyperactivity disorder, inattentive type hereditary diffuse gastric adenocarcinoma IgA glomerulonephritis psoriasis cerebrovascular disorder invasive ductal breast carcinoma cutaneous lupus erythematosus lung cancer

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.