8R8D

Cryo-EM structure of coagulation factor beta-XIIa in complex with the garadacimab Fab fragment (symmetric dimer)

External Resource: Annotation

SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth E], D [auth H]	Heavy Chain	IGHV3	-	coagulation factor xii	SAbDab (2024-08-02)
C [auth I], E [auth L]	Light Chain	IGLV1	Lambda	coagulation factor xii	SAbDab (2024-08-02)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
B [auth E], D [auth H]	Garadacimab	F12	Therapeutic SAbDab (2024-08-02)
C [auth I], E [auth L]	Garadacimab	F12	Therapeutic SAbDab (2024-08-02)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], F [auth A]	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B], F [auth A]	Coagulation factor XII	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding misfolded protein binding peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding misfolded protein 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	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 organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process 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 organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing metabolic process cellular process protein metabolic process macromolecule metabolic process protein activation cascade defense response kinin cascade plasma kallikrein-kinin cascade inflammatory response acute inflammatory response regulation of protein maturation positive regulation of protein maturation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of protein processing regulation of primary metabolic process positive regulation of metabolic process positive regulation of plasminogen activation regulation of proteolysis positive regulation of biosynthetic process regulation of plasminogen activation positive regulation of macromolecule metabolic process plasminogen activation positive regulation of cellular process zymogen activation regulation of biosynthetic process regulation of biological process regulation of protein metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression positive regulation of proteolysis regulation of protein processing regulation of macromolecule biosynthetic process regulation of metabolic process positive regulation of cellular biosynthetic process regulation of response to external stimulus negative regulation of biological process 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 biological process involved in interspecies interaction between organisms immune response response to other organism defense response to symbiont response to biotic stimulus immune system process defense response to other organism innate immune response response to external biotic stimulus regulation of inflammatory response regulation of acute inflammatory response regulation of defense response activation of plasma proteins involved in acute inflammatory response Factor XII activation positive regulation of fibrinolysis regulation of fibrinolysis positive regulation of coagulation positive regulation of blood coagulation positive regulation of response to stimulus positive regulation of hemostasis positive regulation of response to wounding positive regulation of wound healing positive regulation of multicellular organismal process blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation response to misfolded protein response to topologically incorrect protein	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 rough endoplasmic reticulum intracellular organelle intracellular anatomical structure endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system
B [auth E], D [auth H]	Garadacimab heavy chain variable region	-	-	-
C [auth I], E [auth L]	Garadacimab light chain variable region	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B], F [auth A]	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR018056	Kringle, conserved site	Conserved Site
A [auth B], F [auth A]	IPR014394	Coagulation factor XII/hepatocyte growth factor activator	Family
A [auth B], F [auth A]	IPR000562	Fibronectin type II domain	Domain
A [auth B], F [auth A]	IPR000742	EGF-like domain	Domain
A [auth B], F [auth A]	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A [auth B], F [auth A]	IPR013806	Kringle-like fold	Homologous Superfamily
A [auth B], F [auth A]	IPR038178	Kringle superfamily	Homologous Superfamily
A [auth B], F [auth A]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth B], F [auth A]	IPR000083	Fibronectin, type I	Domain
A [auth B], F [auth A]	IPR001314	Peptidase S1A, chymotrypsin family	Family
A [auth B], F [auth A]	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A [auth B], F [auth A]	IPR001254	Serine proteases, trypsin domain	Domain
A [auth B], F [auth A]	IPR001881	EGF-like calcium-binding domain	Domain
A [auth B], F [auth A]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
A [auth B], F [auth A]	IPR050127	Serine Proteases (Peptidase S1 Family)	Family
A [auth B], F [auth A]	IPR000001	Kringle	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], F [auth A]	Pharos: P00748	congenital factor XII deficiency hereditary angioedema hereditary angioedema type 3 angioedema Liver Neoplasms, Experimental hypertensive disorder invasive ductal breast carcinoma lung cancer medulloblastoma ovarian cancer psoriasis breast carcinoma ductal breast carcinoma in situ IgA glomerulonephritis malignant ependymoma congenital factor XII deficiency hereditary angioedema hereditary angioedema type 3 angioedema Liver Neoplasms, Experimental hypertensive disorder invasive ductal breast carcinoma lung cancer medulloblastoma ovarian cancer psoriasis breast carcinoma ductal breast carcinoma in situ IgA glomerulonephritis malignant ependymoma nephrolithiasis pancreatic intraductal papillary-mucinous neoplasm atopic eczema C1 inhibitor deficiency Crohn disease inflammatory bowel disease lung adenocarcinoma malignant glioma non-small cell lung carcinoma pilocytic astrocytoma ulcerative colitis breast cancer chronic kidney disease cystic fibrosis

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 R01GM133198.