5HVG

Crystal Structure of Thrombin-activatable Fibrinolysis Inhibitor in Complex with an Inhibitory Nanobody (VHH-a204)

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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d5hvgb1	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)
B	d5hvgb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
B	d5hvgb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d5hvgd1	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)
D	d5hvgd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	Zn-dependent exopeptidases	8069427	3000662	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-dependent exopeptidases	8069427	3000662	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	PF02244	e5hvgA2	A: a+b two layers	X: Alpha-beta plaits	H: Protease propeptides/inhibitors (From Topology)	T: Protease propeptides/inhibitors	F: PF02244	ECOD (1.6)
A	PF00246	e5hvgA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF00246	ECOD (1.6)
C	PF02244	e5hvgC2	A: a+b two layers	X: Alpha-beta plaits	H: Protease propeptides/inhibitors (From Topology)	T: Protease propeptides/inhibitors	F: PF02244	ECOD (1.6)
C	PF00246	e5hvgC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Zn-dependent exopeptidases (From Topology)	T: Zn-dependent exopeptidases	F: PF00246	ECOD (1.6)
B	PF07686	e5hvgB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e5hvgD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.340	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Metallocarboxypeptidase-like	CATH (4.3.0)
A	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
C	3.30.70.340	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Metallocarboxypeptidase-like	CATH (4.3.0)
C	3.40.630.10	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Zn peptidases	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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, D	VHH-a204	VH	Vicugna pacos (alpaca)	IGHV3S5301, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D	Heavy Chain	IGHV1	-	carboxypeptidase b2	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF02244	Carboxypeptidase activation peptide (Propep_M14)	Carboxypeptidase activation peptide	Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro- ...	Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase, and is responsible for modulation of folding and activity of the pro-enzyme.	Domain
A, C	PF00246	Zinc carboxypeptidase (Peptidase_M14)	Zinc carboxypeptidase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Carboxypeptidase B2	peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding peptidase activity catalytic activity, acting on a protein metallocarboxypeptidase activity hydrolase activity metallopeptidase activity exopeptidase activity catalytic activity metalloexopeptidase activity carboxypeptidase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	multicellular organismal process regulation of hepatocyte proliferation regulation of cellular process gland development negative regulation of biological process liver development multicellular organism development gland morphogenesis anatomical structure development negative regulation of cellular process animal organ morphogenesis epithelial cell proliferation liver morphogenesis system development multicellular organismal process regulation of hepatocyte proliferation regulation of cellular process gland development negative regulation of biological process liver development multicellular organism development gland morphogenesis anatomical structure development negative regulation of cellular process animal organ morphogenesis epithelial cell proliferation liver morphogenesis system development developmental process negative regulation of cell population proliferation regulation of biological process cell population proliferation animal organ development biological regulation epithelial cell proliferation involved in liver morphogenesis anatomical structure morphogenesis hepatocyte proliferation regulation of cell population proliferation hepaticobiliary system development negative regulation of hepatocyte proliferation cellular process regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation response to stimulus response to chemical response to xenobiotic stimulus regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding positive regulation of coagulation regulation of response to external stimulus positive regulation of biological process positive regulation of blood coagulation regulation of response to wounding regulation of coagulation positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding negative regulation of response to stimulus regulation of blood coagulation negative regulation of wound healing negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding negative regulation of hemostasis positive regulation of wound healing fibrinolysis regulation of fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing positive regulation of multicellular organismal process negative regulation of multicellular organismal process negative regulation of fibrinolysis regulation of protein maturation negative regulation of plasminogen activation negative regulation of proteolysis negative regulation of cellular metabolic process protein maturation regulation of primary metabolic process regulation of proteolysis proteolysis organic substance biosynthetic process plasminogen activation negative regulation of protein metabolic process zymogen activation cellular metabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process regulation of protein processing protein processing metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process negative regulation of protein maturation cellular biosynthetic process organic substance metabolic process regulation of plasminogen activation protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process organonitrogen compound metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of protein processing cellular response to stimulus response to organic substance homeostatic process response to monosaccharide response to carbohydrate carbohydrate homeostasis cellular response to hexose stimulus intracellular chemical homeostasis cellular response to monosaccharide stimulus cellular response to organic substance response to oxygen-containing compound cellular response to glucose stimulus intracellular glucose homeostasis cellular response to oxygen-containing compound response to hexose cellular response to carbohydrate stimulus cellular response to chemical stimulus cellular homeostasis chemical homeostasis response to glucose glucose homeostasis regulation of localization regulation of cellular component organization positive regulation of cellular component organization transport positive regulation of extracellular matrix constituent secretion positive regulation of extracellular matrix organization extracellular matrix organization positive regulation of secretion by cell cellular component organization localization regulation of secretion by cell secretion by cell positive regulation of secretion cellular component organization or biogenesis regulation of extracellular matrix constituent secretion positive regulation of cellular process extracellular structure organization regulation of transport secretion export from cell establishment of localization regulation of secretion positive regulation of transport extracellular matrix constituent secretion regulation of extracellular matrix organization external encapsulating structure organization organonitrogen compound catabolic process catabolic process protein catabolic process macromolecule catabolic process organic substance catabolic process animal organ regeneration regeneration liver regeneration	extracellular region cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle
B, D	VHH-a204	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR036990	Metallocarboxypeptidase-like, propeptide	Homologous Superfamily
A, C	IPR033849	Carboxypeptidase B2	Domain
A, C	IPR003146	Carboxypeptidase, activation peptide	Domain
A, C	IPR000834	Peptidase M14, carboxypeptidase A	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: Q96IY4	amenorrhea obesity disorder lung carcinoma ovarian cancer psoriasis lung adenocarcinoma non-small cell lung carcinoma pancreatic ductal adenocarcinoma thrombotic disease lung cancer Postpartum Amenorrhea

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.