4AG4

Crystal structure of a DDR1-Fab complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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 [auth H]	d4ag4h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d4ag4h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4ag4l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d4ag4l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]	PF07654	e4ag4H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth H]	PF07686	e4ag4H1	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)
A	PF21114	e4ag4A4	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Galactose-binding domain-like	F: PF21114	ECOD (1.6)
A	PF00754	e4ag4A3	A: beta sandwiches	X: jelly-roll	H: Galactose-binding domain-like (From Topology)	T: Galactose-binding domain-like	F: PF00754	ECOD (1.6)
C [auth L]	PF07654	e4ag4L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e4ag4L1	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)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.120.260	Mainly Beta	Sandwich	Jelly Rolls	Galactose-binding domain-like	CATH (4.3.0)
A	2.60.120.1190	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C [auth L]	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 [auth H]	3E3, anti-DDR1	VH-CH1	Mus musculus (house mouse)	IGHV1-6101, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202417-0)
C [auth L]	3E3, anti-DDR1	L-KAPPA	Mus musculus (house mouse)	IGKV4-6801, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202417-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	epithelial discoidin domain-containing receptor 1	SAbDab (2024-05-03)
C [auth L]	Light Chain	IGKV4	Kappa	epithelial discoidin domain-containing receptor 1	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00754	F5/8 type C domain (F5_F8_type_C)	F5/8 type C domain	This domain is also known as the discoidin (DS) domain family [1].	Domain
A	PF21114	Discoidin domain-containing receptor 1/2, DS-like domain (DDR1-2_DS-like)	Discoidin domain-containing receptor 1/2, DS-like domain	Discoidin domain-containing receptor 1/2 (DDR1/2) are receptor tyrosine kinases (RTKs) whose activating ligands are various collagens [1,2] and consist of extracellular domains comprising the N-terminal discoidin domain (DS, Pfam:PF00754) followed by ...	Discoidin domain-containing receptor 1/2 (DDR1/2) are receptor tyrosine kinases (RTKs) whose activating ligands are various collagens [1,2] and consist of extracellular domains comprising the N-terminal discoidin domain (DS, Pfam:PF00754) followed by a DS-like domain and the cytoplasmic kinase domain (Pfam:PF07714) 1-3]. Impairment in signaling by DDR1 and DDR2 is associated with the progression of various human diseases, including fibrosis, atherosclerosis and cancer, therefore, inhibition of signaling using monoclonal antibodies (mAbs) may be an useful therapy. This entry represents the DS-like domain, which mediates binding to triple-helical collagen together with the DS domain and contains the epitopes of all mAbs [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	MONOCLONAL ANTIBODY 3E3 HEAVY CHAIN	-	-	-
A	EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1	molecular transducer activity catalytic activity, acting on a protein collagen receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity protein tyrosine kinase collagen receptor activity catalytic activity molecular transducer activity catalytic activity, acting on a protein collagen receptor activity kinase activity protein kinase activity signaling receptor activity transferase activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups protein tyrosine kinase activity transmembrane receptor protein tyrosine kinase activity transmembrane receptor protein kinase activity transmembrane signaling receptor activity protein tyrosine kinase collagen receptor activity catalytic activity collagen binding protein-containing complex binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	organonitrogen compound metabolic process protein phosphorylation protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process peptidyl-tyrosine modification peptidyl-tyrosine autophosphorylation organic substance metabolic process macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process cellular process organonitrogen compound metabolic process protein phosphorylation protein autophosphorylation phosphorylation cellular metabolic process primary metabolic process peptidyl-tyrosine modification peptidyl-tyrosine autophosphorylation organic substance metabolic process macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process metabolic process cellular process protein metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation protein modification process phosphorus metabolic process cell adhesion regulation of biological process regulation of cellular process cell-matrix adhesion regulation of cell-matrix adhesion regulation of cell-substrate adhesion regulation of cell adhesion biological regulation cell-substrate adhesion muscle cell migration cell migration cell motility smooth muscle cell migration developmental process ear development sensory organ development animal organ development anatomical structure development cellular response to stimulus collagen-activated tyrosine kinase receptor signaling pathway cell surface receptor signaling pathway response to stimulus signaling cell surface receptor protein tyrosine kinase signaling pathway cell communication signal transduction collagen-activated signaling pathway enzyme-linked receptor protein signaling pathway cell population proliferation cellular component disassembly extracellular matrix disassembly regulation of cellular component organization extracellular matrix organization cellular component organization cellular component organization or biogenesis regulation of extracellular matrix disassembly regulation of extracellular matrix organization extracellular structure organization external encapsulating structure organization multicellular organismal process cellular developmental process developmental growth cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell growth cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation system development neuron projection extension plasma membrane bounded cell projection organization developmental cell growth growth nervous system development developmental growth involved in morphogenesis generation of neurons anatomical structure morphogenesis neuron development regulation of growth regulation of cell growth positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction regulation of response to stimulus regulation of cell communication phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling axon development multi-multicellular organism process reproductive process female pregnancy embryo implantation multi-organism reproductive process regulation of neuron projection development positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization regulation of cell projection organization regulation of plasma membrane bounded cell projection organization smooth muscle cell-matrix adhesion negative regulation of cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process regulation of body fluid levels secretion transport mammary gland development gland development establishment of localization body fluid secretion localization lactation regulation of biological quality branching involved in mammary gland duct morphogenesis mammary gland morphogenesis branching morphogenesis of an epithelial tube tube morphogenesis gland morphogenesis animal organ morphogenesis epithelial tube morphogenesis epithelium development tube development morphogenesis of an epithelium tissue development mammary gland duct morphogenesis tissue morphogenesis mammary gland epithelium development morphogenesis of a branching structure morphogenesis of a branching epithelium wound healing epiboly involved in wound healing morphogenesis of an epithelial sheet response to stress epiboly wound healing, spreading of cells response to wounding mammary gland lobule development mammary gland alveolus development	extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cellular anatomical entity vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex receptor complex
C [auth L]	MONOCLONAL ANTIBODY 3E3 LIGHT CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR048525	Discoidin domain-containing receptor 1/2, DS-like domain	Domain
A	IPR008266	Tyrosine-protein kinase, active site	Active Site
A	IPR008979	Galactose-binding-like domain superfamily	Homologous Superfamily
A	IPR020635	Tyrosine-protein kinase, catalytic domain	Domain
A	IPR000719	Protein kinase domain	Domain
A	IPR000421	Coagulation factor 5/8 C-terminal domain	Domain
A	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A	IPR002011	Tyrosine-protein kinase, receptor class II, conserved site	Conserved Site
A	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q08345	non-small cell lung carcinoma granular cell carcinoma prostate cancer adenocarcinoma Mammary Neoplasms, Experimental tubular adenocarcinoma squamous cell lung carcinoma duodenal ulcer ovarian cancer peptic esophagitis gastroesophageal reflux disease idiopathic hypereosinophilic syndrome renal cell carcinoma age-related macular degeneration swine influenza non-small cell lung carcinoma granular cell carcinoma prostate cancer adenocarcinoma Mammary Neoplasms, Experimental tubular adenocarcinoma squamous cell lung carcinoma duodenal ulcer ovarian cancer peptic esophagitis gastroesophageal reflux disease idiopathic hypereosinophilic syndrome renal cell carcinoma age-related macular degeneration swine influenza autism spectrum disorder large cell medulloblastoma lung carcinoma thrombocytopenia due to immune destruction chronic eosinophilic leukemia malignant ependymoma cribriform carcinoma of breast Down syndrome oligodendroglioma pancreatic ductal adenocarcinoma peptic ulcer disease gastrointestinal stromal tumor pilocytic astrocytoma Hashimoto thyroiditis idiopathic pulmonary fibrosis schizophrenia astrocytic tumor interstitial lung disease lung adenocarcinoma systemic lupus erythematosus malignant glioma colorectal cancer medullary thyroid gland carcinoma cutaneous lupus erythematosus ductal breast carcinoma in situ oropharynx cancer endogenous depression gastric ulcer glioblastoma primitive neuroectodermal tumor hepatocellular carcinoma psoriatic arthritis interstitial cystitis atypical teratoid rhabdoid tumor invasive ductal breast carcinoma lung benign neoplasm systemic mastocytosis Zollinger-Ellison syndrome chronic myelogenous leukemia, BCR-ABL1 positive cribriform carcinoma membranous glomerulonephritis dermatofibrosarcoma protuberans

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.