3N1M

Crystal Structure of IhhN bound to BOCFn3

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)
A [auth B]	d3n1mb_	Alpha and beta proteins (a+b)	Hedgehog/DD-peptidase	Hedgehog/DD-peptidase	Hedgehog (development protein), N-terminal signaling domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3n1mc_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	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 [auth B]	SCOP2B Superfamily	Hedgehog/DD-peptidase	8084201	3001458	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Fibronectin type III	8086427	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 [auth B]	HH_signal	e3n1mB1	A: a+b two layers	X: Hedgehog/DD-peptidase (From Topology)	H: Hedgehog/DD-peptidase (From Topology)	T: Hedgehog/DD-peptidase	F: HH_signal	ECOD (1.6)
B [auth C]	fn3	e3n1mC1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth B]	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C]	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	Indian hedgehog protein	patched binding protein binding binding signaling receptor binding cation binding ion binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cholesterol-protein transferase activity patched binding protein binding binding signaling receptor binding cation binding ion binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity cholesterol-protein transferase activity transferase activity	developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment primary metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process connective tissue development animal organ development endochondral bone morphogenesis tissue development multicellular organism development anatomical structure morphogenesis skeletal system development chondrocyte differentiation involved in endochondral bone morphogenesis anatomical structure development chondrocyte differentiation skeletal system morphogenesis animal organ morphogenesis cartilage development involved in endochondral bone morphogenesis bone morphogenesis bone development system development cartilage development cell adhesion cell-cell adhesion epithelial cell-cell adhesion embryonic skeletal joint development chordate embryonic development embryo development embryo development ending in birth or egg hatching embryonic skeletal system development head development head morphogenesis body morphogenesis epithelium development sensory organ development eye development retinal pigment epithelium development retina development in camera-type eye visual system development camera-type eye development sensory system development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation regulation of macromolecule metabolic process regulation of gene expression regulation of macromolecule biosynthetic process regulation of metabolic process regulation of growth growth signaling cell-cell signaling cell communication in utero embryonic development cell population proliferation chondrocyte proliferation branching morphogenesis of an epithelial tube angiogenesis tube morphogenesis epithelial tube morphogenesis blood vessel development blood vessel morphogenesis tube development morphogenesis of an epithelium vasculature development circulatory system development branching involved in blood vessel morphogenesis tissue morphogenesis morphogenesis of a branching structure anatomical structure formation involved in morphogenesis morphogenesis of a branching epithelium intein-mediated protein splicing protein splicing negative regulation of lymphocyte proliferation regulation of leukocyte differentiation regulation of leukocyte activation negative regulation of biological process regulation of cell activation negative regulation of T cell differentiation in thymus mononuclear cell differentiation regulation of cell differentiation lymphocyte differentiation negative regulation of T cell proliferation regulation of cell development negative regulation of cell adhesion T cell differentiation in thymus negative regulation of T cell differentiation negative regulation of leukocyte proliferation T cell activation lymphocyte proliferation T cell differentiation regulation of immune system process regulation of immature T cell proliferation negative regulation of hemopoiesis regulation of leukocyte proliferation negative regulation of immature T cell proliferation negative regulation of leukocyte differentiation regulation of immature T cell proliferation in thymus negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion regulation of cell population proliferation mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of lymphocyte differentiation negative regulation of multicellular organismal process negative regulation of leukocyte activation leukocyte differentiation regulation of developmental process immature T cell proliferation in thymus cell development regulation of T cell differentiation in thymus lymphocyte activation negative regulation of lymphocyte activation leukocyte cell-cell adhesion leukocyte proliferation leukocyte activation regulation of T cell differentiation negative regulation of mononuclear cell proliferation negative regulation of cellular process regulation of multicellular organismal process regulation of cell-cell adhesion negative regulation of cell differentiation negative regulation of immature T cell proliferation in thymus T cell proliferation regulation of lymphocyte proliferation regulation of lymphocyte differentiation regulation of multicellular organismal development negative regulation of cell population proliferation hemopoiesis negative regulation of developmental process regulation of cell adhesion cell activation regulation of T cell activation immature T cell proliferation negative regulation of cell activation negative regulation of cell development regulation of T cell proliferation negative regulation of immune system process immune system process regulation of hemopoiesis regulation of mononuclear cell proliferation regulation of lymphocyte activation embryonic eye morphogenesis embryonic camera-type eye development eye morphogenesis embryonic organ development embryonic organ morphogenesis camera-type eye morphogenesis embryonic morphogenesis embryonic camera-type eye morphogenesis sensory organ morphogenesis multicellular organism growth developmental growth positive regulation of biological process collagen biosynthetic process regulation of collagen biosynthetic process regulation of collagen metabolic process positive regulation of metabolic process positive regulation of collagen metabolic process positive regulation of biosynthetic process positive regulation of collagen biosynthetic process collagen metabolic process positive regulation of cellular process positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of DNA-templated transcription multicellular organismal-level homeostasis homeostatic process tissue remodeling bone remodeling anatomical structure homeostasis tissue homeostasis bone resorption heart morphogenesis pattern specification process embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry determination of left/right symmetry specification of symmetry heart development determination of heart left/right asymmetry regionalization left/right pattern formation regulation of alpha-beta T cell activation positive regulation of T cell differentiation positive regulation of developmental process positive regulation of cell activation positive regulation of leukocyte activation alpha-beta T cell activation positive regulation of immune system process positive regulation of T cell activation positive regulation of cell development positive regulation of alpha-beta T cell activation positive regulation of multicellular organismal process positive regulation of alpha-beta T cell differentiation positive regulation of leukocyte cell-cell adhesion regulation of alpha-beta T cell differentiation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation alpha-beta T cell differentiation positive regulation of hemopoiesis positive regulation of cell differentiation positive regulation of cell adhesion positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation carbohydrate derivative metabolic process proteoglycan metabolic process glycoprotein metabolic process self proteolysis ossification osteoblast differentiation cellular response to stimulus cell surface receptor signaling pathway response to stimulus smoothened signaling pathway signal transduction negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death multi-multicellular organism process maternal process involved in female pregnancy reproductive process multicellular organismal reproductive process female pregnancy multi-organism reproductive process positive regulation of cell communication positive regulation of signal transduction regulation of signal transduction positive regulation of response to stimulus positive regulation of smoothened signaling pathway regulation of smoothened signaling pathway regulation of signaling regulation of response to stimulus regulation of cell communication positive regulation of signaling cell morphogenesis epithelial cell differentiation epithelial cell development epithelial cell morphogenesis positive regulation of mesenchymal cell proliferation positive regulation of cell population proliferation regulation of mesenchymal cell proliferation mesenchymal cell proliferation gland development animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration positive regulation of epithelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation positive regulation of T cell differentiation in thymus eye pigmentation developmental pigmentation regulation of developmental pigmentation regulation of pigmentation negative regulation of eye pigmentation pigmentation negative regulation of developmental pigmentation regulation of eye pigmentation anatomical structure maturation cell maturation developmental maturation negative regulation of alpha-beta T cell differentiation negative regulation of alpha-beta T cell activation pancreas development response to mechanical stimulus response to abiotic stimulus response to external stimulus egg coat formation vitelline membrane formation sexual reproduction cellular component assembly involved in morphogenesis cellular process involved in reproduction in multicellular organism extracellular matrix organization developmental process involved in reproduction female gamete generation gamete generation cellular component organization cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly cellular component organization or biogenesis extracellular matrix assembly extracellular structure organization oogenesis germ cell development external encapsulating structure organization digestive system development embryonic digestive tract morphogenesis digestive tract development digestive tract morphogenesis embryonic digestive tract development muscle tissue development smooth muscle tissue development regulation of cartilage development regulation of chondrocyte differentiation negative regulation of cartilage development negative regulation of chondrocyte differentiation embryonic pattern specification photoreceptor cell differentiation camera-type eye photoreceptor cell fate commitment neural retina development neurogenesis neuron differentiation eye photoreceptor cell differentiation photoreceptor cell fate commitment eye photoreceptor cell fate commitment neuron fate commitment nervous system development camera-type eye photoreceptor cell differentiation generation of neurons retina morphogenesis in camera-type eye neuron development response to lipid response to chemical response to estradiol response to oxygen-containing compound response to organic cyclic compound limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis embryonic digit morphogenesis limb morphogenesis somite development	membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane extracellular region membrane-bounded organelle Golgi membrane intracellular anatomical structure Golgi apparatus membrane intracellular membrane-bounded organelle endomembrane system intracellular organelle bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane extracellular region extracellular space cell periphery plasma membrane extracellular matrix external encapsulating structure organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
B [auth C]	Brother of CDO	-	developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development developmental process regulation of biological process regulation of cellular process regulation of developmental process cellular developmental process biological regulation positive regulation of biological process regulation of cell differentiation positive regulation of myoblast differentiation muscle structure development positive regulation of developmental process positive regulation of cell differentiation cell differentiation anatomical structure development regulation of myoblast differentiation cellular process myoblast differentiation positive regulation of cellular process multicellular organismal process axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis system development plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development cell adhesion cell-cell adhesion	growth cone axon cell projection cellular anatomical structure distal axon neuron projection axonal growth cone plasma membrane bounded cell projection site of polarized growth cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth B]	IPR036844	Hint domain superfamily	Homologous Superfamily
A [auth B]	IPR003586	Hint domain C-terminal	Domain
A [auth B]	IPR003587	Hint domain N-terminal	Domain
A [auth B]	IPR000320	Hedgehog, N-terminal signalling domain	Domain
A [auth B]	IPR001657	Hedgehog protein	Family
A [auth B]	IPR006141	Intein N-terminal splicing region	PTM
A [auth B]	IPR001767	Hedgehog protein, Hint domain	Domain
A [auth B]	IPR050387	Hedgehog Signaling	Family
A [auth B]	IPR009045	Hedgehog signalling/DD-peptidase zinc-binding domain superfamily	Homologous Superfamily
B [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth C]	IPR003598	Immunoglobulin subtype 2	Domain
B [auth C]	IPR003961	Fibronectin type III	Domain
B [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth C]	IPR003599	Immunoglobulin domain subtype	Domain
B [auth C]	IPR007110	Immunoglobulin-like domain	Domain
B [auth C]	IPR013098	Immunoglobulin I-set	Domain
B [auth C]	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B]	Pharos: Q14623	acrocapitofemoral dysplasia brachydactyly type A1A gastrointestinal stromal tumor brachydactyly type A1 endometriosis Crohn disease osteosarcoma psoriasis brachydactyly corpus luteum cyst Endometrioma intellectual disability ovarian cyst ulcerative colitis craniosynostosis acrocapitofemoral dysplasia brachydactyly type A1A gastrointestinal stromal tumor brachydactyly type A1 endometriosis Crohn disease osteosarcoma psoriasis brachydactyly corpus luteum cyst Endometrioma intellectual disability ovarian cyst ulcerative colitis craniosynostosis osteogenesis imperfecta
B [auth C]	Pharos: Q9BWV1	colorectal cancer gastrointestinal stromal tumor osteosarcoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma breast cancer glioblastoma invasive ductal breast carcinoma malignant glioma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma astrocytic tumor colorectal cancer gastrointestinal stromal tumor osteosarcoma pancreatic intraductal papillary-mucinous carcinoma psoriasis adrenal cortex carcinoma breast cancer glioblastoma invasive ductal breast carcinoma malignant glioma medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm subependymal giant cell astrocytoma astrocytic tumor breast carcinoma dilated cardiomyopathy idiopathic scoliosis lung carcinoma Malignant neoplasm of breast oligodendroglioma pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia atypical teratoid rhabdoid tumor colorectal adenoma interstitial lung disease malignant ependymoma malignant pancreatic neoplasm

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.