6RVC | pdb_00006rvc

Crystal structure of Patched-1 ectodomain 2 (PTCH1-ECD2) in complex with nanobody 75

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d6rvcd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6rvcd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d6rvcd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d6rvce1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d6rvce3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E	d6rvce2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d6rvcf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d6rvcf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d6rvcf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	V-set_12	e6rvcD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
E	V-set_12	e6rvcE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F	V-set_12	e6rvcF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D, E, F	Heavy Chain	IGHV1	-	protein patched homolog 1	SAbDab (2025-05-09)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Protein patched homolog 1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity hedgehog receptor activity protein-containing complex binding binding patched binding protein binding signaling receptor binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity hedgehog receptor activity protein-containing complex binding binding patched binding protein binding signaling receptor binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cyclin binding hedgehog family protein binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding smoothened binding G protein-coupled receptor binding	positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process positive regulation of cholesterol efflux regulation of localization transport positive regulation of sterol transport positive regulation of biological process regulation of lipid transport organic hydroxy compound transport localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport positive regulation of cholesterol transport regulation of sterol transport regulation of biological process regulation of transport biological regulation lipid localization lipid transport positive regulation of lipid localization establishment of localization positive regulation of lipid transport positive regulation of transport regulation of lipid localization macromolecule localization cholesterol transport cholesterol efflux response to stimulus response to chemical response to xenobiotic stimulus cellular response to stimulus response to sterol response to lipid response to alcohol response to oxygen-containing compound response to cholesterol cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol cellular response to lipid cellular process cellular response to sterol cellular response to cholesterol developmental process multicellular organism development multicellular organismal process head development central nervous system development anatomical structure development animal organ development brain development nervous system development system development cell population proliferation cell proliferation involved in kidney development renal system development metanephros development cell proliferation involved in metanephros development kidney development mammary gland epithelial cell differentiation epithelium development cellular developmental process mammary gland development gland development tissue development epithelial cell differentiation mammary gland epithelium development cell differentiation reproductive system development prostate gland development reproductive process urogenital system development developmental process involved in reproduction reproductive structure development dorsal/ventral pattern formation pattern specification process regionalization epithelial cell proliferation keratinocyte proliferation protein localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization localization within membrane protein localization to membrane tube development mammary gland morphogenesis morphogenesis of an epithelium mammary gland duct morphogenesis tissue morphogenesis anatomical structure morphogenesis tube morphogenesis gland morphogenesis animal organ morphogenesis epithelial tube morphogenesis embryo development ending in birth or egg hatching pharyngeal system development chordate embryonic development embryo development response to chlorate in utero embryonic development limb development appendage development appendage morphogenesis limb morphogenesis regulation of multicellular organism growth regulation of growth regulation of developmental growth negative regulation of multicellular organism growth regulation of developmental process developmental growth negative regulation of developmental process growth negative regulation of biological process multicellular organism growth negative regulation of developmental growth negative regulation of growth regulation of multicellular organismal process negative regulation of multicellular organismal process heart development heart morphogenesis circulatory system development embryonic organ development collecting duct development metanephric collecting duct development negative regulation of cell population proliferation regulation of stem cell proliferation regulation of cellular process negative regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation negative regulation of cellular process embryonic epithelial tube formation tube formation epithelial tube formation primary neural tube formation morphogenesis of embryonic epithelium neural tube development embryonic morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure 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 regulation of keratinocyte proliferation negative regulation of keratinocyte proliferation regulation of epithelial cell proliferation negative regulation of epithelial cell proliferation dorsal/ventral neural tube patterning neural tube patterning RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development ureteric bud morphogenesis branching involved in ureteric bud morphogenesis renal tubule development nephron development nephron epithelium development ureteric bud development mesonephros development kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium negative regulation of cell division cell division regulation of cell division chemical homeostasis homeostatic process glucose homeostasis carbohydrate homeostasis regulation of epidermal cell differentiation epidermis development regulation of cell differentiation regulation of epithelial cell differentiation positive regulation of developmental process positive regulation of cell differentiation positive regulation of cellular process regulation of multicellular organismal development epidermal cell differentiation positive regulation of epidermis development positive regulation of epithelial cell differentiation regulation of epidermis development positive regulation of epidermal cell differentiation cell differentiation involved in kidney development cell surface receptor signaling pathway signaling smoothened signaling pathway cell communication signal transduction negative regulation of DNA-binding transcription factor activity negative regulation of molecular function regulation of molecular function regulation of DNA-binding transcription factor activity regulation of mitotic cell cycle cell cycle regulation of cell cycle mitotic cell cycle regulation of osteoblast differentiation negative regulation of osteoblast differentiation osteoblast differentiation ossification negative regulation of cell differentiation regulation of signaling regulation of signal transduction regulation of response to stimulus regulation of cell communication regulation of smoothened signaling pathway cell differentiation in spinal cord generation of neurons central nervous system neuron differentiation neurogenesis spinal cord development neuron differentiation ventral spinal cord development spinal cord motor neuron differentiation animal organ regeneration liver development regeneration hepaticobiliary system development liver regeneration protein maturation proteolysis protein processing protein metabolic process response to retinoic acid negative regulation of signaling negative regulation of cell communication negative regulation of smoothened signaling pathway negative regulation of response to stimulus negative regulation of signal transduction commissural neuron axon guidance axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development embryonic limb morphogenesis embryonic appendage morphogenesis cell fate specification cell fate commitment epidermal cell fate specification cell fate determination response to mechanical stimulus response to abiotic stimulus response to external stimulus regulation of protein localization regulation of cellular localization positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process neural plate pattern specification embryonic pattern specification embryonic axis specification neural plate development neural plate axis specification axis specification muscle tissue development smooth muscle tissue development hindlimb morphogenesis response to estradiol somite development	cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane apical part of cell dendrite terminus axon neuron projection cell periphery postsynapse cellular anatomical structure postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region synaptic membrane apical part of cell dendrite terminus axon neuron projection plasma membrane bounded cell projection growth cone somatodendritic compartment cell projection distal axon dendritic growth cone dendrite dendritic tree site of polarized growth membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle perinuclear region of cytoplasm midbody axonal growth cone membrane microdomain membrane raft plasma membrane raft caveola cilium ciliary membrane cell projection membrane
D, E, F	Nanobody NB75	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR000731	Sterol-sensing domain	Domain
A, B, C	IPR053958	HMGCR/SNAP/NPC1-like, sterol-sensing domain	Domain
A, B, C	IPR004766	Transmembrane receptor, patched	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: Q13635	nevoid basal cell carcinoma syndrome medulloblastoma holoprosencephaly 7 rhabdomyosarcoma holoprosencephaly skin basal cell carcinoma cleft palate Craniofacial Abnormalities adult medulloblastoma medulloepithelioma cleft lip monosomy 9q22.3 ependymoblastoma HIV infectious disease skin neoplasm nevoid basal cell carcinoma syndrome medulloblastoma holoprosencephaly 7 rhabdomyosarcoma holoprosencephaly skin basal cell carcinoma cleft palate Craniofacial Abnormalities adult medulloblastoma medulloepithelioma cleft lip monosomy 9q22.3 ependymoblastoma HIV infectious disease skin neoplasm malignant pancreatic neoplasm cerebral primitive neuroectodermal tumor medullomyoblastoma with myogenic differentiation gastrointestinal stromal tumor skin cancer cancer childhood medulloblastoma melanotic medulloblastoma osteosarcoma endometriosis pancreatic neoplasm gastric cancer psoriasis semilobar holoprosencephaly basal cell carcinoma skin disease basal cell carcinoma, susceptibility to, 1 interstitial cystitis brain disease lung cancer breast cancer cataract desmoplastic/nodular medulloblastoma ovarian cancer gastric carcinoma alobar holoprosencephaly hydrocephalus invasive ductal breast carcinoma squamous cell carcinoma malignant mesothelioma breast carcinoma coloboma endogenous depression pancreatic ductal adenocarcinoma focal dermal hypoplasia primitive neuroectodermal tumor atypical teratoid rhabdoid tumor intellectual disability skin pigmented basal cell carcinoma subependymal giant cell astrocytoma brain cancer lobar holoprosencephaly

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Multi-Drug Efflux Transporters	2:1 human Ptch1-SHH-N complex (revised structure)

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.