1UJ3

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor

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	d1uj3a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin light chain kappa variable domain, VL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d1uj3a2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin light chain kappa constant domain, CL-kappa	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1uj3b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d1uj3b2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d1uj3c1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	Extracellular region of human tissue factor	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Fibronectin type III	8055099	3002063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fibronectin type III	8055493	3002063	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	C1-set_4	e1uj3A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A	V-set	e1uj3A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B	V-set_8	e1uj3B1	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)
B	C1-set_1	e1uj3B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
C	Tissue_fac	e1uj3C2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Tissue_fac	ECOD (1.6)
C	Interfer-bind_2	e1uj3C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Interfer-bind_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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
A	HATR-5	L-KAPPA	Homo sapiens (human)	IGKV1D-1601, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-4_KAPPA	IMGT (202415-0)
B	HATR-5	VH-CH1	Homo sapiens (human)	IGHV1-4601, IGHV1-4602, IGHV1-4603, IGHJ401, IGHJ402, IGHJ403, IGHG401, IGHG404	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-4_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A	Light Chain	IGKV1D	Kappa	tissue factor	SAbDab (2024-04-19)
B	Heavy Chain	IGHV1	-	tissue factor	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF01108	Tissue factor (Tissue_fac)	Tissue factor	-	Family
C	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	IgG Fab light chain	-	-	-
B	IgG Fab heavy chain	-	-	-
C	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 organic substance metabolic process biosynthetic process response to stress proteolysis organic substance biosynthetic process 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 organic substance metabolic process biosynthetic process response to stress proteolysis organic substance biosynthetic process 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 response to organic substance regulation of cellular process cell surface receptor signaling pathway signaling response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance 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	IPR001187	Tissue factor	Family
C	IPR003961	Fibronectin type III	Domain
C	IPR015373	Interferon/interleukin receptor domain	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
C	IPR030472	Tissue factor, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P13726	acute promyelocytic leukemia breast carcinoma nephrotic syndrome thrombotic thrombocytopenic purpura Venous Thrombosis coronary artery disease disseminated intravascular coagulation thrombotic disease cirrhosis of liver breast cancer drug-induced liver injury spina bifida heart disease inborn carbohydrate metabolic disorder kidney disease acute promyelocytic leukemia breast carcinoma nephrotic syndrome thrombotic thrombocytopenic purpura Venous Thrombosis coronary artery disease disseminated intravascular coagulation thrombotic disease cirrhosis of liver breast cancer drug-induced liver injury spina bifida heart disease inborn carbohydrate metabolic disorder kidney disease lung adenocarcinoma atherosclerosis autoimmune disease nasopharyngeal carcinoma cervical carcinoma pancreatic ductal adenocarcinoma pneumonia pulmonary embolism thrombocytopenia hereditary von Willebrand disease tuberculosis interstitial lung disease large cell medulloblastoma adult acute respiratory distress syndrome lung cancer atopic eczema malignant pancreatic neoplasm Barrett esophagus medulloblastoma cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia COVID-19 primitive neuroectodermal tumor sinusitis thrombophilia hypertensive disorder ulcerative colitis invasive ductal breast carcinoma liver disease anemia lung carcinoma atypical teratoid rhabdoid tumor myocardial ischemia cerebrovascular disorder ovarian cancer congenital thrombotic thrombocytopenic purpura pituitary cancer psoriasis

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.