5N48

Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d5n48b_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5n48d1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5n48d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5n48a_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	Neutrophil gelatinase-associated lipocalin (NGAL)	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5n48c_	All beta proteins	Lipocalins	Lipocalins	Retinol binding protein-like	Neutrophil gelatinase-associated lipocalin (NGAL)	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)
A	SCOP2B Superfamily	Lipocalins	8033646	3001332	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Lipocalins	8033646	3001332	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)
B	fn3	e5n48B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3	ECOD (1.6)
D	fn3	e5n48D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3	ECOD (1.6)
A	Lipocalin_2	e5n48A1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin_2	ECOD (1.6)
C	Lipocalin_2	e5n48C1	A: beta barrels	X: Lipocalins/Streptavidin	H: Lipocalins (From Topology)	T: Lipocalins	F: Lipocalin_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
A	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)
C	2.40.128.20	Mainly Beta	Beta Barrel	Lipocalin	Calycin beta-barrel core domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain	-	Domain
A, C	PF00061	Lipocalin / cytosolic fatty-acid binding protein family (Lipocalin)	Lipocalin / cytosolic fatty-acid binding protein family	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid ...	Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The family also encompasses the enzyme prostaglandin D synthase (EC:5.3.99.2). Alignment subsumes both the lipocalin and fatty acid binding protein signatures from PROSITE. This is supported on structural and functional grounds. The structure is an eight-stranded beta barrel.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Fibronectin	enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity identical protein binding protein binding binding signaling receptor binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity enzyme binding enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity identical protein binding protein binding binding signaling receptor binding signaling receptor regulator activity receptor ligand activity signaling receptor activator activity enzyme binding protease binding collagen binding protein-containing complex binding cell adhesion molecule binding integrin binding structural molecule activity extracellular matrix structural constituent proteoglycan binding carbohydrate derivative binding heparin binding glycosaminoglycan binding sulfur compound binding	response to stimulus response to activity response to muscle activity regulation of transforming growth factor beta production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process transforming growth factor beta production negative regulation of macromolecule metabolic process regulation of biosynthetic process response to stimulus response to activity response to muscle activity regulation of transforming growth factor beta production multicellular organismal process regulation of cellular process negative regulation of biological process regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process transforming growth factor beta production negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process negative regulation of transforming growth factor beta production regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process developmental process heart development multicellular organism development anatomical structure development animal organ development circulatory system development system development positive regulation of locomotion regulation of cell motility regulation of substrate-dependent cell migration, cell attachment to substrate positive regulation of biological process positive regulation of cell migration cell adhesion positive regulation of cell-substrate adhesion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process regulation of cell-substrate adhesion positive regulation of cell adhesion regulation of cell adhesion cell-substrate adhesion regulation of locomotion substrate-dependent cell migration substrate-dependent cell migration, cell attachment to substrate positive regulation of substrate-dependent cell migration, cell attachment to substrate cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly integrin activation cellular component organization or biogenesis positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of gene expression positive regulation of biosynthetic process positive regulation of macromolecule metabolic process substrate adhesion-dependent cell spreading monocyte activation regulation of leukocyte activation cell activation regulation of cell activation negative regulation of monocyte activation myeloid leukocyte activation leukocyte activation negative regulation of cell activation negative regulation of immune system process immune system process regulation of immune system process negative regulation of leukocyte activation axon extension positive regulation of nervous system development regulation of growth axonogenesis regulation of cellular component size developmental growth cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization regulation of biological quality positive regulation of developmental growth regulation of cell projection organization positive regulation of cell development nervous system development developmental growth involved in morphogenesis generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension regulation of nervous system development neurogenesis regulation of extent of cell growth positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis positive regulation of axon extension positive regulation of axonogenesis regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth growth positive regulation of cell growth axon development regulation of cell growth cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis positive regulation of growth neuron development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size calcium-independent cell-matrix adhesion cell-matrix adhesion acute-phase response defense response response to stress inflammatory response acute inflammatory response response to wounding cellular response to stimulus regulation of signaling signaling regulation of signal transduction regulation of MAPK cascade intracellular signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette MAPK cascade regulation of cell communication ERK1 and ERK2 cascade signal transduction regulation of ERK1 and ERK2 cascade blood vessel morphogenesis tube development angiogenesis vasculature development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration autonomic nervous system development neural crest cell migration stem cell development neural crest cell differentiation tissue development stem cell differentiation neural crest cell migration involved in autonomic nervous system development mesenchymal cell differentiation formation of primary germ layer embryonic morphogenesis embryo development gastrulation endoderm development endoderm formation endodermal cell differentiation fibroblast proliferation cell population proliferation positive regulation of cell population proliferation regulation of fibroblast proliferation regulation of cell population proliferation positive regulation of fibroblast proliferation integrin-mediated signaling pathway cell surface receptor signaling pathway positive regulation of cell communication regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signal transduction positive regulation of response to stimulus positive regulation of intracellular signal transduction positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction phosphatidylinositol 3-kinase/protein kinase B signal transduction positive regulation of signaling biological process involved in interspecies interaction between organisms biological process involved in interaction with symbiont biological process involved in symbiotic interaction regulation of cell shape regulation of cell morphogenesis cell junction organization cell junction assembly cell-substrate junction assembly cell-substrate junction organization wound healing regulation of protein modification process regulation of protein phosphorylation regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process protein modification process phosphorus metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process macromolecule modification regulation of phosphorylation regulation of phosphorus metabolic process peptide cross-linking	basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure collagen-containing extracellular matrix extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular 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 endoplasmic reticulum cytoplasm vesicle lumen intracellular vesicle cytoplasmic vesicle lumen secretory granule lumen cytoplasmic vesicle secretory granule secretory vesicle platelet alpha granule platelet alpha granule lumen endoplasmic reticulum-Golgi intermediate compartment protein-containing complex fibrinogen complex apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane blood microparticle
A, C	Neutrophil gelatinase-associated lipocalin	molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding molecular sequestering activity iron ion sequestering activity metal ion sequestering activity cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding organic cyclic compound binding anion binding macrolide binding heterocyclic compound binding enterobactin binding identical protein binding protein binding	multicellular organismal process regulation of biological process regulation of cellular process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process multicellular organismal process regulation of biological process regulation of cellular process homeostatic process biological regulation positive regulation of biological process adaptive thermogenesis positive regulation of metabolic process multicellular organismal-level homeostasis regulation of cold-induced thermogenesis cold-induced thermogenesis temperature homeostasis positive regulation of cold-induced thermogenesis positive regulation of multicellular organismal process cellular process metabolic process regulation of multicellular organismal process regulation of metabolic process positive regulation of cellular process apoptotic process cell death programmed cell death biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus defense response to bacterium response to bacterium siderophore transport localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport iron coordination entity transport	cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cellular anatomical structure extracellular region extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle extracellular space vesicle extracellular membrane-bounded organelle vesicle lumen intracellular anatomical structure intracellular vesicle membrane-enclosed lumen cytoplasmic vesicle lumen intracellular membrane-bounded organelle secretory granule lumen endomembrane system intracellular organelle lumen intracellular organelle cytoplasmic vesicle organelle lumen specific granule lumen secretory granule secretory vesicle cytoplasm specific granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR000562	Fibronectin type II domain	Domain
B, D	IPR000083	Fibronectin, type I	Domain
B, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D	IPR036943	Fibronectin type II domain superfamily	Homologous Superfamily
B, D	IPR013806	Kringle-like fold	Homologous Superfamily
B, D	IPR003961	Fibronectin type III	Domain
B, D	IPR050991	Extracellular Matrix Regulatory Proteins	Family
B, D	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A, C	IPR012674	Calycin	Homologous Superfamily
A, C	IPR003087	Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12	Family
A, C	IPR002345	Lipocalin	Family
A, C	IPR000566	Lipocalin/cytosolic fatty-acid binding domain	Domain
A, C	IPR022272	Lipocalin family conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	Pharos: P02751	glioblastoma hypertensive disorder Crohn disease malignant mesothelioma aortic valve insufficiency breast carcinoma pulmonary fibrosis focal segmental glomerulosclerosis giant cell glioblastoma Mammary Neoplasms, Experimental carcinoma spondylometaphyseal dysplasia, 'corner fracture' type ureteral obstruction glomerulopathy with fibronectin deposits 2 heart disease glioblastoma hypertensive disorder Crohn disease malignant mesothelioma aortic valve insufficiency breast carcinoma pulmonary fibrosis focal segmental glomerulosclerosis giant cell glioblastoma Mammary Neoplasms, Experimental carcinoma spondylometaphyseal dysplasia, 'corner fracture' type ureteral obstruction glomerulopathy with fibronectin deposits 2 heart disease diabetes mellitus sarcomatoid carcinoma breast cancer ileocolitis ovarian cancer interstitial lung disease polycystic ovary syndrome kidney disease diabetic kidney disease limb-girdle muscular dystrophy schizophrenia Duchenne muscular dystrophy lung disease alcohol abuse transitional cell carcinoma endometriosis undifferentiated carcinoma atherosclerosis glomerulopathy with fibronectin deposits 1 autoimmune disease myocardial infarction oligodendroglioma colorectal cancer pancreatic ductal adenocarcinoma Crohn's colitis invasive ductal breast carcinoma primitive neuroectodermal tumor cystic fibrosis large cell medulloblastoma liver disease ductal breast carcinoma in situ malignant ependymoma tuberculosis fibronectin glomerulopathy gastric carcinoma arthritic joint disease atopic eczema Becker muscular dystrophy nasopharyngeal carcinoma breast disease hydrolethalus syndrome nephrosclerosis idiopathic interstitial pneumonia osteosarcoma coronary artery disease inborn carbohydrate metabolic disorder pilocytic astrocytoma juvenile dermatomyositis pterygium lung carcinoma adrenal cortex carcinoma Ehlers-Danlos syndrome malignant glioma ulcerative colitis Gaucher disease malignant pancreatic neoplasm astrocytic tumor mammary neoplasms, animal atypical teratoid rhabdoid tumor medulloblastoma hematologic disease cancer
A, C	Pharos: P80188	rheumatoid arthritis beta thalassemia kidney disease adult acute respiratory distress syndrome Inflammation cancer contact dermatitis heart valve disease calcinosis cutaneous lupus erythematosus ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma acute kidney failure ulcerative colitis rheumatoid arthritis beta thalassemia kidney disease adult acute respiratory distress syndrome Inflammation cancer contact dermatitis heart valve disease calcinosis cutaneous lupus erythematosus ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia gastric carcinoma acute kidney failure ulcerative colitis benign neoplasm lung cancer chronic renal failure syndrome malignant pancreatic neoplasm nasopharyngeal carcinoma non-small cell lung carcinoma cystic fibrosis pancreatic ductal adenocarcinoma pituitary cancer exocrine pancreatic carcinoma schizophrenia head and neck cancer thalassemia minor hepatocellular carcinoma interstitial cystitis lung carcinoma MALT lymphoma Crohn disease osteosarcoma pancreatic intraductal papillary-mucinous neoplasm drug-induced liver injury psoriasis gastric cancer sinusitis hepatitis, non-human animal astrocytic tumor hereditary persistence of fetal hemoglobin lung adenocarcinoma chronic obstructive pulmonary disease malignant mesothelioma

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 R01GM157729.