8CN9

Factor VII binding Fab of the bispecific antibody HMB-001 in complex with Factor VII

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Trypsin-like serine proteases	8003776	3000114	SCOP2B (2021-05-27)
R	SCOP2B Superfamily	Trypsin-like serine proteases	8003776	3000114	SCOP2B (2021-05-27)
C	SCOP2B Superfamily	Trypsin-like serine proteases	8003776	3000114	SCOP2B (2021-05-27)
M	SCOP2B Superfamily	Trypsin-like serine proteases	8003776	3000114	SCOP2B (2021-05-27)
I	SCOP2B Superfamily	EGF/Laminin-like	8039292	3000412	SCOP2B (2021-05-27)
I	SCOP2B Superfamily	EGF/Laminin-like	8039297	3000412	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	EGF/Laminin-like	8039297	3000412	SCOP2B (2021-05-27)
D	SCOP2B Superfamily	EGF/Laminin-like	8039292	3000412	SCOP2B (2021-05-27)
N	SCOP2B Superfamily	EGF/Laminin-like	8039292	3000412	SCOP2B (2021-05-27)
N	SCOP2B Superfamily	EGF/Laminin-like	8039297	3000412	SCOP2B (2021-05-27)
S	SCOP2B Superfamily	EGF/Laminin-like	8039292	3000412	SCOP2B (2021-05-27)
S	SCOP2B Superfamily	EGF/Laminin-like	8039297	3000412	SCOP2B (2021-05-27)
E	SCOP2B Superfamily	Fibronectin type III	8055099	3002063	SCOP2B (2021-05-27)
E	SCOP2B Superfamily	Fibronectin type III	8055493	3002063	SCOP2B (2021-05-27)
J	SCOP2B Superfamily	Fibronectin type III	8055493	3002063	SCOP2B (2021-05-27)
J	SCOP2B Superfamily	Fibronectin type III	8055099	3002063	SCOP2B (2021-05-27)
O	SCOP2B Superfamily	Fibronectin type III	8055099	3002063	SCOP2B (2021-05-27)
T	SCOP2B Superfamily	Fibronectin type III	8055099	3002063	SCOP2B (2021-05-27)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A, F, K, P	Light Chain	IGKV3	Kappa	coagulation factor vii \| coagulation factor vii	SAbDab (2024-07-12)
B, G, L, Q	Heavy Chain	IGHV4	-	coagulation factor vii \| coagulation factor vii	SAbDab (2024-07-12)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, H, M, R	PF00089	Trypsin (Trypsin)	Trypsin	-	Domain
D, I, N, S	PF00008	EGF-like domain (EGF)	EGF-like domain	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is t ...	There is no clear separation between noise and signal. Pfam:PF00053 is very similar, but has 8 instead of 6 conserved cysteines. Includes some cytokine receptors. The EGF domain misses the N-terminus regions of the Ca2+ binding EGF domains (this is the main reason of discrepancy between swiss-prot domain start/end and Pfam). The family is hard to model due to many similar but different sub-types of EGF domains. Pfam certainly misses a number of EGF domains.	Domain
D, I, N, S	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
E, J, O, T	PF09294	Interferon-alpha/beta receptor, fibronectin type III (Interfer-bind)	Interferon-alpha/beta receptor, fibronectin type III	Members of this family adopt a secondary structure consisting of seven beta-strands arranged in an immunoglobulin-like beta-sandwich, in a Greek-key topology. They are required for binding to interferon-alpha [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, F, K, P	Fab light chain	-	-	-
B, G, L, Q	Fab heavy chain	-	-	-
C, H, M, R	Coagulation factor VII	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 cation binding ion binding binding calcium ion binding metal ion binding small molecule 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 cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor 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 response to lipid response to chemical response to astaxanthin 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 response to lipid response to chemical response to astaxanthin cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling response to sterol response to alcohol response to oxygen-containing compound response to cholesterol response to organic cyclic compound response to thyrotropin-releasing hormone response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to nitrogen compound response to carbon dioxide response to thyroid hormone response to thyroxine response to amino acid response to L-phenylalanine derivative response to acid chemical response to growth hormone response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of coagulation regulation of response to external stimulus positive regulation of blood coagulation regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of wound healing positive regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to external stimulus taxis positive regulation of cell motility regulation of cell migration cell migration regulation of immune system process cell motility positive regulation of immune system process locomotion cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration regulation of chemotaxis leukocyte migration cellular response to chemical stimulus immune system process regulation of locomotion leukocyte chemotaxis regulation of platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of platelet-derived growth factor receptor signaling pathway cell surface receptor signaling pathway platelet-derived growth factor receptor signaling pathway rhythmic process circadian rhythm response to estrogen organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process response to Thyroid stimulating hormone response to glycoprotein response to 2,3,7,8-tetrachlorodibenzodioxine positive chemotaxis positive regulation of positive chemotaxis regulation of positive chemotaxis response to phenylpropanoid response to ketone response to hydroxyisoflavone response to genistein developmental process animal organ regeneration animal organ development anatomical structure development regeneration response to nutrient levels response to nutrient response to vitamin K response to vitamin response to estradiol	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space vesicle plasma membrane membrane Golgi apparatus Golgi lumen protein-containing complex catalytic complex peptidase complex serine-type peptidase complex
D, I, N, S	Coagulation factor VII	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 cation binding ion binding binding calcium ion binding metal ion binding small molecule 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 cation binding ion binding binding calcium ion binding metal ion binding small molecule binding protein binding signaling receptor 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 response to lipid response to chemical response to astaxanthin 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 response to lipid response to chemical response to astaxanthin cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction positive regulation of TOR signaling signal transduction positive regulation of cellular process TOR signaling regulation of biological process regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of response to stimulus regulation of cell communication cellular process positive regulation of signaling response to sterol response to alcohol response to oxygen-containing compound response to cholesterol response to organic cyclic compound response to thyrotropin-releasing hormone response to hormone response to endogenous stimulus response to organonitrogen compound response to peptide hormone response to nitrogen compound response to carbon dioxide response to thyroid hormone response to thyroxine response to amino acid response to L-phenylalanine derivative response to acid chemical response to growth hormone response to decreased oxygen levels response to hypoxia response to oxygen levels response to abiotic stimulus positive regulation of coagulation regulation of response to external stimulus positive regulation of blood coagulation regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of blood coagulation response to external stimulus positive regulation of wound healing regulation of wound healing positive regulation of multicellular organismal process positive regulation of locomotion regulation of cell motility positive regulation of chemotaxis positive regulation of cell migration positive regulation of response to external stimulus taxis positive regulation of cell motility regulation of cell migration cell migration regulation of immune system process cell motility positive regulation of immune system process locomotion cell chemotaxis chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of leukocyte chemotaxis positive regulation of leukocyte migration regulation of chemotaxis leukocyte migration cellular response to chemical stimulus immune system process regulation of locomotion leukocyte chemotaxis regulation of platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of platelet-derived growth factor receptor signaling pathway cell surface receptor signaling pathway platelet-derived growth factor receptor signaling pathway rhythmic process circadian rhythm response to estrogen organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process response to Thyroid stimulating hormone response to glycoprotein response to 2,3,7,8-tetrachlorodibenzodioxine positive chemotaxis positive regulation of positive chemotaxis regulation of positive chemotaxis response to phenylpropanoid response to ketone response to hydroxyisoflavone response to genistein developmental process animal organ regeneration animal organ development anatomical structure development regeneration response to nutrient levels response to nutrient response to vitamin K response to vitamin response to estradiol	cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen cell periphery extracellular matrix external encapsulating structure collagen-containing extracellular matrix cellular anatomical entity membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cytoplasm extracellular region extracellular space vesicle plasma membrane membrane Golgi apparatus Golgi lumen protein-containing complex catalytic complex peptidase complex serine-type peptidase complex
E, J, O, T	Tissue factor	protein binding binding enzyme binding protease binding phospholipid binding lipid binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity cytokine receptor activity immune receptor activity	organonitrogen compound metabolic process response to stimulus defense response cellular biosynthetic process cellular metabolic process activation of plasma proteins involved in acute inflammatory response primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process response to stress proteolysis protein processing organonitrogen compound metabolic process response to stimulus defense response cellular biosynthetic process cellular metabolic process activation of plasma proteins involved in acute inflammatory response primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process response to stress proteolysis protein processing metabolic process cellular process inflammatory response protein metabolic process macromolecule metabolic process acute inflammatory response multicellular organismal process regulation of body fluid levels wound healing hemostasis biological regulation blood coagulation 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 regulation of response to stress regulation of multicellular organismal process positive regulation of hemostasis regulation of hemostasis positive regulation of response to wounding regulation of biological process regulation of blood coagulation response to external stimulus activation of blood coagulation via clotting cascade positive regulation of wound healing regulation of response to stimulus regulation of wound healing positive regulation of multicellular organismal process cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular response to cytokine stimulus signal transduction regulation of catalytic activity positive regulation of protein metabolic process positive regulation of peptidase activity positive regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of primary metabolic process positive regulation of molecular function positive regulation of metabolic process regulation of cysteine-type endopeptidase activity involved in apoptotic process regulation of proteolysis regulation of endopeptidase activity positive regulation of macromolecule metabolic process activation of cysteine-type endopeptidase activity involved in apoptotic process regulation of cysteine-type endopeptidase activity regulation of protein metabolic process regulation of peptidase activity positive regulation of catalytic activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of hydrolase activity positive regulation of cysteine-type endopeptidase activity regulation of hydrolase activity positive regulation of endopeptidase activity positive regulation of proteolysis regulation of metabolic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of cellular metabolic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cellular biosynthetic process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction intracellular signal transduction regulation of intracellular signal transduction positive regulation of TOR signaling TOR signaling regulation of signaling regulation of TOR signaling positive regulation of intracellular signal transduction regulation of cell communication positive regulation of signaling positive regulation of interleukin-8 production cytokine production regulation of cytokine production interleukin-8 production positive regulation of cytokine production regulation of interleukin-8 production positive chemotaxis chemotaxis positive regulation of locomotion positive regulation of positive chemotaxis regulation of chemotaxis positive regulation of chemotaxis regulation of positive chemotaxis positive regulation of response to external stimulus taxis regulation of locomotion locomotion regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process multicellular organism development tube morphogenesis anatomical structure development regulation of anatomical structure morphogenesis blood vessel development system development developmental process regulation of multicellular organismal development blood vessel morphogenesis tube development positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis regulation of cell motility positive regulation of cell migration positive regulation of cell motility regulation of cell migration cell migration cell motility cell population proliferation positive regulation of cell population proliferation endothelial cell proliferation positive regulation of epithelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation positive regulation of endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation regulation of platelet-derived growth factor receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway enzyme-linked receptor protein signaling pathway positive regulation of platelet-derived growth factor receptor signaling pathway platelet-derived growth factor receptor signaling pathway	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular matrix external encapsulating structure collagen-containing extracellular matrix protein-containing complex catalytic complex peptidase complex serine-type peptidase complex cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane extracellular matrix external encapsulating structure collagen-containing extracellular matrix protein-containing complex catalytic complex peptidase complex serine-type peptidase complex extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, H, M, R	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
C, H, M, R	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
C, H, M, R	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C, H, M, R	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
C, H, M, R	IPR001254	Serine proteases, trypsin domain	Domain
C, H, M, R	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
C, H, M, R	IPR001881	EGF-like calcium-binding domain	Domain
C, H, M, R	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
C, H, M, R	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
C, H, M, R	IPR000742	EGF-like domain	Domain
C, H, M, R	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
C, H, M, R	IPR001314	Peptidase S1A, chymotrypsin family	Family
C, H, M, R	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
C, H, M, R	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
D, I, N, S	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
D, I, N, S	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
D, I, N, S	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
D, I, N, S	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
D, I, N, S	IPR001254	Serine proteases, trypsin domain	Domain
D, I, N, S	IPR035972	Gamma-carboxyglutamic acid-rich (GLA) domain superfamily	Homologous Superfamily
D, I, N, S	IPR001881	EGF-like calcium-binding domain	Domain
D, I, N, S	IPR012224	Peptidase S1A, coagulation factor VII/IX/X/C/Z	Family
D, I, N, S	IPR000294	Gamma-carboxyglutamic acid-rich (GLA) domain	Domain
D, I, N, S	IPR000742	EGF-like domain	Domain
D, I, N, S	IPR017857	Coagulation factor-like, Gla domain superfamily	Homologous Superfamily
D, I, N, S	IPR001314	Peptidase S1A, chymotrypsin family	Family
D, I, N, S	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
D, I, N, S	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
E, J, O, T	IPR001187	Tissue factor	Family
E, J, O, T	IPR003961	Fibronectin type III	Domain
E, J, O, T	IPR015373	Interferon/interleukin receptor domain	Domain
E, J, O, T	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E, J, O, T	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
E, J, O, T	IPR030472	Tissue factor, conserved site	Conserved Site