3N1F | pdb_00003n1f

Crystal Structure of IhhN bound to CDOFn3

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)
D	d3n1fd1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3n1fd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3n1fc_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3n1fb_	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)
A	d3n1fa_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Fibronectin type III	8086313	3002063	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fibronectin type III	8086313	3002063	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Hedgehog/DD-peptidase	8084201	3001458	SCOP2B (2022-06-29)
A	SCOP2 Family	Hedgehog (development protein), N-terminal signaling domain	8084200	4001392	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Hedgehog/DD-peptidase	8084201	3001458	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	PBP	e3n1fD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
C	Col-Pyo_DNase	e3n1fC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: DEATH domain	T: DEATH domain	F: Col-Pyo_DNase	ECOD (v294.1)
B	PBP	e3n1fB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)
A	PBP	e3n1fA1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Immunoglobulin-related	T: PEBP-like	F: PBP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
A	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	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
C, D	Cell adhesion molecule-related/down-regulated by oncogenes	molecular transducer activity coreceptor activity signaling receptor activity	regulation of muscle tissue development multicellular organismal process regulation of developmental process skeletal muscle tissue development positive regulation of skeletal muscle tissue development positive regulation of biological process regulation of skeletal muscle tissue development striated muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development positive regulation of muscle organ development anatomical structure development regulation of multicellular organismal process regulation of muscle tissue development multicellular organismal process regulation of developmental process skeletal muscle tissue development positive regulation of skeletal muscle tissue development positive regulation of biological process regulation of skeletal muscle tissue development striated muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development positive regulation of muscle organ development anatomical structure development regulation of multicellular organismal process muscle tissue development muscle organ development developmental process regulation of biological process animal organ development biological regulation positive regulation of striated muscle tissue development regulation of striated muscle tissue development tissue development positive regulation of muscle tissue development regulation of muscle organ development positive regulation of multicellular organismal process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment neuroblast proliferation cell population proliferation nervous system development generation of neurons neurogenesis multicellular organism development neural precursor cell proliferation system development cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling smoothened signaling pathway cell communication signal transduction camera-type eye morphogenesis sensory organ development eye development embryonic morphogenesis visual system development retina development in camera-type eye embryo development retina morphogenesis in camera-type eye anatomical structure morphogenesis eye morphogenesis embryonic retina morphogenesis in camera-type eye sensory organ morphogenesis camera-type eye development animal organ morphogenesis sensory system development skeletal muscle cell differentiation skeletal muscle satellite cell differentiation lens development in camera-type eye negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process Wnt signaling pathway regulation of signaling regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication central nervous system neuron differentiation central nervous system development neuron differentiation response to nutrient levels response to lipid response to nutrient response to oxygen-containing compound response to vitamin cellular response to oxygen-containing compound cellular response to vitamin D cellular response to nutrient levels cellular response to chemical stimulus response to vitamin D cellular response to vitamin response to chemical cellular response to lipid cellular response to nutrient head development forebrain development brain development pallium development cerebral cortex development telencephalon development positive regulation of cell communication positive 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 positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade positive regulation of signaling regulation of cell differentiation positive regulation of neuron differentiation positive regulation of cell differentiation regulation of neuron differentiation embryonic body morphogenesis body morphogenesis cell adhesion myoblast fusion cell-cell fusion muscle cell differentiation myotube differentiation syncytium formation by plasma membrane fusion anatomical structure formation involved in morphogenesis syncytium formation striated muscle cell differentiation regulation of multicellular organismal development negative regulation of developmental process negative regulation of biomineral tissue development regulation of biomineral tissue development biomineral tissue development cell-cell adhesion small GTPase-mediated signal transduction regulation of small GTPase mediated signal transduction positive regulation of small GTPase mediated signal transduction positive regulation of nervous system development positive regulation of cell population proliferation regulation of neuroblast proliferation cell development regulation of neurogenesis regulation of cell development regulation of nervous system development positive regulation of neurogenesis regulation of neural precursor cell proliferation positive regulation of cell development positive regulation of neural precursor cell proliferation regulation of cell population proliferation positive regulation of neuroblast proliferation 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 positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II primary metabolic process regulation of macromolecule metabolic process positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process anterior/posterior pattern specification pattern specification process regionalization	cell periphery cellular anatomical structure plasma membrane membrane
A, 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 negative regulation of lymphocyte differentiation regulation of leukocyte cell-cell adhesion 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 negative regulation of cell differentiation regulation of cell-cell adhesion 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 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C, D	IPR003598	Immunoglobulin subtype 2	Domain
C, D	IPR003599	Immunoglobulin domain subtype	Domain
C, D	IPR013098	Immunoglobulin I-set	Domain
C, D	IPR003961	Fibronectin type III	Domain
C, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C, D	IPR007110	Immunoglobulin-like domain	Domain
C, D	IPR036116	Fibronectin type III superfamily	Homologous Superfamily
A, B	IPR036844	Hint domain superfamily	Homologous Superfamily
A, B	IPR009045	Peptidase M74/Hedgehog-like, zinc-binding domain superfamily	Homologous Superfamily
A, B	IPR003586	Hint domain C-terminal	Domain
A, B	IPR003587	Hint domain N-terminal	Domain
A, B	IPR000320	Hedgehog, N-terminal signalling domain	Domain
A, B	IPR001657	Hedgehog protein	Family
A, B	IPR006141	Intein N-terminal splicing region	PTM
A, B	IPR001767	Hedgehog protein, Hint domain	Domain
A, B	IPR050387	Hedgehog Signaling	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: Q4KMG0	holoprosencephaly 11 holoprosencephaly gastrointestinal stromal tumor pituitary stalk interruption syndrome osteosarcoma psoriasis transitional cell carcinoma adrenoleukodystrophy breast cancer ductal breast carcinoma in situ lobar holoprosencephaly lung carcinoma medulloblastoma ovarian cancer semilobar holoprosencephaly holoprosencephaly 11 holoprosencephaly gastrointestinal stromal tumor pituitary stalk interruption syndrome osteosarcoma psoriasis transitional cell carcinoma adrenoleukodystrophy breast cancer ductal breast carcinoma in situ lobar holoprosencephaly lung carcinoma medulloblastoma ovarian cancer semilobar holoprosencephaly alobar holoprosencephaly cystic fibrosis intellectual disability lung adenocarcinoma malignant colon neoplasm oligodendroglioma subependymal giant cell astrocytoma atypical teratoid rhabdoid tumor Duchenne muscular dystrophy invasive ductal breast carcinoma lung cancer malignant ependymoma
A, 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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.