3N1Q

Crystal Structure of DhhN 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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth B]	d3n1qb_	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)
C [auth A]	d3n1qa_	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)
E	d3n1qe_	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]	d3n1qc_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3n1qd_	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	Fibronectin type III	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3n1qf_	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	8084199	3001458	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Hedgehog/DD-peptidase	8084199	3001458	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Hedgehog/DD-peptidase	8084199	3001458	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Fibronectin type III	8086313	3002063	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Fibronectin type III	8086313	3002063	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Fibronectin type III	8086313	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	e3n1qB1	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)
C [auth A]	HH_signal	e3n1qA1	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)
E	HH_signal	e3n1qE1	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	e3n1qC1	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	e3n1qD1	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)
F	fn3	e3n1qF1	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)
C [auth A]	3.30.1380.10	Alpha Beta	2-Layer Sandwich	Muramoyl-pentapeptide Carboxypeptidase	domain 2	CATH (4.3.0)
E	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)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	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
A [auth B], C [auth A], E	PF01085	Hedgehog amino-terminal signalling domain (HH_signal)	Hedgehog amino-terminal signalling domain	For the carboxyl Hint module, see Pfam:PF01079. Hedgehog is a family of secreted signal molecules required for embryonic cell differentiation.	Domain
A [auth B], C [auth A], E	PF01079	Hint module (Hint)	Hint module	-	Family
B [auth C], D, F	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], C [auth A], E	Desert hedgehog protein	cation binding ion binding 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 transition metal ion binding zinc ion binding cation binding ion binding 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 transition metal ion binding zinc ion binding patched binding protein binding signaling receptor binding	developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment organic substance metabolic process organonitrogen compound metabolic process proteolysis self proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process developmental process cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment organic substance metabolic process organonitrogen compound metabolic process proteolysis self proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process multicellular organismal process ossification osteoblast differentiation regulation of biosynthetic process regulation of steroid biosynthetic process regulation of biological process regulation of lipid metabolic process steroid metabolic process regulation of steroid metabolic process biological regulation lipid biosynthetic process regulation of primary metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process regulation of lipid biosynthetic process steroid biosynthetic process regulation of metabolic process lipid metabolic process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development Leydig cell differentiation system development cellular biosynthetic process cellular metabolic process gene expression macromolecule biosynthetic process protein maturation protein autoprocessing protein processing cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling smoothened signaling pathway cell communication signal transduction response to organic substance response to hormone response to chemical response to endogenous stimulus response to estrogen sex determination male sex determination regulation of cellular metabolic process regulation of macromolecule metabolic process regulation of cellular biosynthetic process regulation of gene expression regulation of macromolecule biosynthetic process positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to stimulus positive regulation of smoothened signaling pathway positive regulation of cellular process regulation of smoothened signaling pathway regulation of signaling regulation of response to stimulus regulation of cell communication positive regulation of signaling cell-cell signaling spermatid development spermatid differentiation sexual reproduction spermatogenesis multicellular organismal reproductive process cell development cellular process involved in reproduction in multicellular organism gamete generation male gamete generation germ cell development myelination axon ensheathment ensheathment of neurons nervous system development response to lipid response to estradiol response to oxygen-containing compound response to organic cyclic compound	cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cell periphery plasma membrane membrane cellular anatomical entity membrane-bounded organelle intracellular anatomical structure organelle subcompartment intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum membrane Golgi membrane Golgi apparatus bounding membrane of organelle extracellular region extracellular space
B [auth C], D, F	Cell adhesion molecule-related/down-regulated by oncogenes	-	developmental process regulation of muscle tissue development regulation of biological process regulation of developmental process skeletal muscle tissue development positive regulation of skeletal muscle tissue development animal organ development biological regulation positive regulation of biological process tissue development regulation of skeletal muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development positive regulation of muscle tissue development developmental process regulation of muscle tissue development regulation of biological process regulation of developmental process skeletal muscle tissue development positive regulation of skeletal muscle tissue development animal organ development biological regulation positive regulation of biological process tissue development regulation of skeletal muscle tissue development muscle structure development positive regulation of developmental process skeletal muscle organ development positive regulation of muscle tissue development anatomical structure development muscle tissue development muscle organ development cellular developmental process cell differentiation cellular process cell fate specification cell fate commitment neuroblast proliferation multicellular organismal process 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 neuron differentiation head development forebrain development brain development pallium development cerebral cortex development central nervous system development telencephalon development positive regulation of cell communication positive regulation of signal transduction 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 MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication 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 positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process metabolic process regulation of phosphorylation macromolecule metabolic process regulation of metabolic process 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 multicellular organismal process regulation of neural precursor cell proliferation regulation of multicellular organismal development positive regulation of cell development positive regulation of neural precursor cell proliferation regulation of cell population proliferation positive regulation of multicellular organismal process positive regulation of neuroblast proliferation positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of transcription by RNA polymerase II positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of biosynthetic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process anterior/posterior pattern specification pattern specification process regionalization	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth B], C [auth A], E	Pharos: O43323	46,XY complete gonadal dysgenesis 46,XY gonadal dysgenesis-motor and sensory neuropathy syndrome 46,XY sex reversal 7 Charcot-Marie-Tooth disease osteoporosis attention deficit hyperactivity disorder, inattentive type Disorders of Sex Development bipolar disorder gonadal dysgenesis
B [auth C], D, F	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

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.