8Z39 | pdb_00008z39

Crystal structure of Sonic hedgehog in complex with antibody 5E1 mutant L-T56A with metals

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Hedgehog/DD-peptidase	8084197	3001458	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	sonic hedgehog protein n-product	SAbDab (2025-11-07)
C [auth L]	Light Chain	IGKV6	Kappa	sonic hedgehog protein n-product	SAbDab (2025-11-07)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth H]	Heavy chain of antibody 5E1	-	-	-
C [auth L]	Light chain of antibody 5E1	-	-	-
A	Sonic hedgehog protein N-product	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity morphogen activity receptor ligand activity signaling receptor activator activity patched binding cation binding ion binding calcium ion binding metal ion binding protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity signaling receptor regulator activity morphogen activity receptor ligand activity signaling receptor activator activity patched 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 endopeptidase activity glycosaminoglycan binding carbohydrate derivative binding extracellular matrix binding laminin-1 binding laminin binding transition metal ion binding zinc ion binding	developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process heart development animal organ development circulatory system development system development thymic T cell selection cellular developmental process hemopoiesis cell activation cell development developmental process multicellular organism development multicellular organismal process anatomical structure development pattern specification process heart development animal organ development circulatory system development system development thymic T cell selection cellular developmental process hemopoiesis cell activation cell development mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process cell differentiation negative thymic T cell selection T cell differentiation cellular process negative T cell selection T cell selection leukocyte differentiation tube development respiratory tube development right lung development lung development respiratory system development digestive system development foregut morphogenesis embryonic morphogenesis embryo development digestive tract development anatomical structure morphogenesis tube morphogenesis embryonic foregut morphogenesis digestive tract morphogenesis cellular response to stimulus mesenchymal smoothened signaling pathway involved in prostate gland development regulation of cellular process epithelial-mesenchymal signaling involved in prostate gland development response to stimulus signaling prostate gland development reproductive process gland development developmental process involved in reproduction epithelial-mesenchymal cell signaling cell communication reproductive structure development signal transduction regulation of biological process reproductive system development cell surface receptor signaling pathway biological regulation cell-cell signaling urogenital system development smoothened signaling pathway regulation of developmental process positive regulation of biological process regulation of cell differentiation regulation of striated muscle cell differentiation muscle cell differentiation positive regulation of muscle cell differentiation muscle structure development positive regulation of developmental process regulation of muscle cell differentiation positive regulation of cell differentiation positive regulation of striated muscle cell differentiation striated muscle cell differentiation positive regulation of cellular process epithelium development branching morphogenesis of an epithelial tube morphogenesis of an epithelium tissue development tissue morphogenesis morphogenesis of a branching structure epithelial tube morphogenesis morphogenesis of a branching epithelium myoblast differentiation canonical Wnt signaling pathway Wnt signaling pathway negative regulation of biological process neurogenesis neuron differentiation regulation of dopaminergic neuron differentiation negative regulation of cellular process negative regulation of dopaminergic neuron differentiation negative regulation of cell differentiation dopaminergic neuron differentiation negative regulation of developmental process nervous system development generation of neurons negative regulation of neuron differentiation regulation of neuron differentiation dorsal/ventral pattern formation regionalization positive regulation of cerebellar granule cell precursor proliferation positive regulation of cell population proliferation regulation of cerebellar granule cell precursor proliferation cell proliferation in external granule layer cell proliferation in hindbrain regulation of neural precursor cell proliferation head development cell population proliferation brain development positive regulation of neural precursor cell proliferation central nervous system development regulation of cell population proliferation cerebellar granule cell precursor proliferation neural precursor cell proliferation hindbrain development negative regulation of lymphocyte proliferation regulation of leukocyte activation regulation of cell activation negative regulation of T cell proliferation negative regulation of cell adhesion negative regulation of leukocyte proliferation lymphocyte proliferation regulation of immune system process regulation of leukocyte proliferation negative regulation of T cell activation negative regulation of leukocyte cell-cell adhesion mononuclear cell proliferation negative regulation of cell-cell adhesion regulation of leukocyte cell-cell adhesion negative regulation of multicellular organismal process negative regulation of leukocyte activation negative regulation of lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion negative regulation of mononuclear cell proliferation cell adhesion cell-cell adhesion regulation of multicellular organismal process regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation negative regulation of cell population proliferation regulation of cell adhesion regulation of T cell activation negative regulation of cell activation regulation of T cell proliferation negative regulation of immune system process regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of animal organ morphogenesis regulation of odontogenesis odontogenesis animal organ morphogenesis regulation of anatomical structure morphogenesis genitalia development sex differentiation male sex differentiation male genitalia development epidermis development molting cycle process hair cycle epidermis morphogenesis skin development skin epidermis development hair follicle development molting cycle hair cycle process hair follicle morphogenesis embryonic hindlimb morphogenesis limb development appendage development embryonic limb morphogenesis hindlimb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis regulation of localization localization regulation of protein localization macromolecule localization protein localization to organelle regulation of protein localization to nucleus intracellular protein localization protein localization to nucleus catabolic process negative regulation of proteolysis negative regulation of proteolysis involved in protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process negative regulation of protein catabolic process regulation of proteolysis involved in protein catabolic process regulation of proteolysis modification-dependent macromolecule catabolic process proteolysis protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of ubiquitin-dependent protein catabolic process negative regulation of catabolic process negative regulation of proteasomal ubiquitin-dependent protein catabolic process regulation of protein metabolic process negative regulation of metabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process regulation of macromolecule metabolic process regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process negative regulation of proteasomal protein catabolic process regulation of proteasomal protein catabolic process ubiquitin-dependent protein catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process renal system development metanephros development collecting duct development metanephric collecting duct development kidney development blastoderm segmentation segmentation neural crest cell development mesenchyme development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation embryonic pattern specification trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation mesenchymal cell proliferation involved in lung development mesenchymal cell proliferation skeletal muscle cell differentiation skeletal muscle tissue development myotube differentiation striated muscle tissue development skeletal muscle organ development skeletal muscle fiber differentiation muscle tissue development muscle organ development angiogenesis blood vessel development blood vessel morphogenesis vasculature development branching involved in blood vessel morphogenesis anatomical structure formation involved in morphogenesis intein-mediated protein splicing gene expression macromolecule biosynthetic process protein maturation biosynthetic process protein processing protein splicing epithelial cell proliferation involved in prostate gland development epithelial cell proliferation sclerotome development positive regulation of sclerotome development somite development regulation of sclerotome development negative regulation of locomotion regulation of cell motility regulation of locomotion regulation of cell migration negative regulation of cell motility negative regulation of cell migration locomotion negative regulation of sterol transport transport regulation of lipid transport negative regulation of transport organic hydroxy compound transport negative regulation of lipid localization regulation of cholesterol efflux sterol transport regulation of cholesterol transport regulation of sterol transport negative regulation of lipid transport regulation of transport lipid localization lipid transport negative regulation of cholesterol transport establishment of localization regulation of lipid localization negative regulation of cholesterol efflux cholesterol transport cholesterol efflux negative regulation of mesenchymal cell apoptotic process mesenchymal cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of mesenchymal cell apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death regulation of mesenchymal cell proliferation involved in prostate gland development regulation of mesenchymal cell proliferation mesenchymal cell proliferation involved in prostate gland development RNA 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 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 nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription negative regulation of RNA metabolic process smooth muscle cell differentiation positive regulation of smooth muscle cell differentiation regulation of smooth muscle cell differentiation ureter smooth muscle development smooth muscle tissue development ureter smooth muscle cell differentiation ureter development regulation of ureter smooth muscle cell differentiation regulation of muscle organ development positive regulation of ureter smooth muscle cell differentiation positive regulation of multicellular organismal process regulation of leukocyte differentiation regulation of alpha-beta T cell activation positive regulation of T cell differentiation regulation of cell development 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 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 regulation of T cell differentiation positive regulation of lymphocyte activation alpha-beta T cell differentiation positive regulation of hemopoiesis regulation of lymphocyte differentiation regulation of multicellular organismal development positive regulation of cell adhesion regulation of hemopoiesis positive regulation of leukocyte differentiation positive regulation of lymphocyte differentiation hindgut morphogenesis hindgut development salivary gland cavitation salivary gland development tube formation gland morphogenesis salivary gland morphogenesis tube lumen cavitation exocrine system development formation of anatomical boundary lung lobe morphogenesis lung lobe development lung morphogenesis thyroid gland development endocrine system development positive thymic T cell selection positive T cell selection 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 tracheoesophageal septum formation regulation of reproductive process regulation of epithelial cell proliferation involved in prostate gland development positive regulation of reproductive process positive regulation of epithelial cell proliferation positive regulation of epithelial cell proliferation involved in prostate gland development regulation of epithelial cell proliferation positive regulation of T cell differentiation in thymus regulation of T cell differentiation in thymus forebrain development diencephalon development thalamus development negative regulation of T cell differentiation negative regulation of hemopoiesis negative regulation of leukocyte differentiation negative regulation of lymphocyte differentiation negative regulation of alpha-beta T cell differentiation negative regulation of cell development negative regulation of alpha-beta T cell activation telencephalon regionalization forebrain regionalization telencephalon development vasculogenesis 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 animal organ formation apoptotic signaling pathway negative regulation of T cell differentiation in thymus negative regulation of gene expression lateral mesoderm development determination of left/right asymmetry in lateral mesoderm determination of bilateral symmetry determination of left/right symmetry left/right pattern formation mesoderm development specification of symmetry positive regulation of skeletal muscle cell proliferation muscle cell proliferation skeletal muscle cell proliferation regulation of skeletal muscle cell proliferation striated muscle cell proliferation intermediate filament organization intermediate filament-based process organelle organization supramolecular fiber organization cytoskeleton organization intermediate filament cytoskeleton organization embryonic digit morphogenesis left lung development positive regulation of nervous system development astrocyte differentiation regulation of neurogenesis regulation of gliogenesis regulation of astrocyte differentiation positive regulation of gliogenesis regulation of nervous system development gliogenesis positive regulation of neurogenesis positive regulation of astrocyte differentiation regulation of glial cell differentiation positive regulation of glial cell differentiation glial cell differentiation ectoderm development regulation of muscle tissue development positive regulation of skeletal muscle tissue development regulation of skeletal muscle tissue development positive regulation of muscle organ development positive regulation of striated muscle tissue development regulation of striated muscle tissue development positive regulation of muscle tissue development regulation of body fluid levels wound healing hemostasis blood coagulation response to stress coagulation regulation of biological quality response to wounding cell fate specification cell fate commitment neuroblast proliferation protein autoprocessing cellular response to metal ion cellular response to chemical stimulus response to lithium ion cellular response to lithium ion response to metal ion response to chemical limb bud formation negative regulation of kidney smooth muscle cell differentiation regulation of kidney smooth muscle cell differentiation negative regulation of muscle cell differentiation kidney smooth muscle cell differentiation negative regulation of smooth muscle cell differentiation cell differentiation involved in kidney development kidney smooth muscle tissue development embryonic forelimb morphogenesis forelimb morphogenesis CD4-positive or CD8-positive, alpha-beta T cell lineage commitment T cell lineage commitment regulation of hormone levels steroid metabolic process androgen metabolic process hormone metabolic process lipid metabolic process 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 ear development sensory organ development inner ear development negative regulation of signaling regulation of canonical Wnt signaling pathway negative regulation of cell communication negative regulation of Wnt signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway transcription elongation by RNA polymerase II negative regulation of transcription elongation by RNA polymerase II regulation of DNA-templated transcription elongation regulation of transcription elongation by RNA polymerase II negative regulation of DNA-templated transcription, elongation DNA-templated transcription elongation establishment of cell polarity establishment of epithelial cell polarity establishment or maintenance of cell polarity artery development establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport nuclear transport intracellular transport import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell protein import into nucleus intracellular protein transport developmental growth organ growth prostate gland epithelium morphogenesis prostate gland morphogenetic growth prostate gland growth axis elongation branch elongation of an epithelium growth developmental growth involved in morphogenesis prostate gland morphogenesis primary prostatic bud elongation kidney mesenchymal cell proliferation metanephric mesenchyme development metanephric mesenchymal cell proliferation involved in metanephros development cell proliferation involved in kidney development kidney mesenchyme development cell proliferation involved in metanephros development positive regulation of cell division cell division regulation of cell division positive regulation of nucleocytoplasmic transport positive regulation of establishment of protein localization positive regulation of protein transport regulation of protein import into nucleus positive regulation of intracellular transport regulation of intracellular transport positive regulation of protein localization to nucleus regulation of establishment of protein localization positive regulation of protein import into nucleus regulation of nucleocytoplasmic transport regulation of protein transport positive regulation of transport regulation of cellular localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport ventral midline development negative regulation of ureter smooth muscle cell differentiation trachea morphogenesis trachea development positive regulation of Wnt signaling pathway stem cell proliferation activin receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway regulation of transmembrane receptor protein serine/threonine kinase signaling pathway nodal signaling pathway regulation of nodal signaling pathway transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway enzyme-linked receptor protein signaling pathway embryo development ending in birth or egg hatching skeletal system development chordate embryonic development embryonic skeletal system development branching involved in prostate gland morphogenesis prostate epithelial cord elongation neural tube development dorsal/ventral neural tube patterning neural tube patterning regulation of immature T cell proliferation positive regulation of immature T cell proliferation positive regulation of lymphocyte proliferation regulation of immature T cell proliferation in thymus positive regulation of T cell proliferation positive regulation of leukocyte proliferation immature T cell proliferation in thymus positive regulation of mononuclear cell proliferation positive regulation of immature T cell proliferation in thymus immature T cell proliferation mesonephric epithelium development kidney epithelium development nephron morphogenesis 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 mesonephric tubule morphogenesis mesonephric tubule development renal tubule morphogenesis positive regulation of DNA-templated transcription positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis heart looping embryonic organ development embryonic organ morphogenesis determination of heart left/right asymmetry midbrain development self proteolysis immune system development hematopoietic or lymphoid organ development thymus development bud outgrowth involved in lung branching epithelial tube branching involved in lung morphogenesis oligodendrocyte differentiation lung-associated mesenchyme development lung epithelium development positive regulation of mesenchymal cell proliferation involved in ureter development regulation of mesenchymal cell proliferation involved in ureter development positive regulation of mesenchymal cell proliferation mesenchymal cell proliferation involved in ureter development eye development visual system development camera-type eye development sensory system development odontogenesis of dentin-containing tooth import into cell endocytosis vesicle-mediated transport epithelial cell proliferation involved in salivary gland morphogenesis cell differentiation in spinal cord central nervous system neuron differentiation spinal cord development ventral spinal cord development spinal cord motor neuron differentiation spinal cord dorsal/ventral patterning spinal cord patterning neuron fate commitment osteoblast development ossification osteoblast differentiation lymphoid progenitor cell differentiation hematopoietic progenitor cell differentiation Bergmann glial cell differentiation regulation of stem cell proliferation oligodendrocyte development glial cell development pancreas development polarity specification of anterior/posterior axis specification of axis polarity anterior/posterior pattern specification anterior/posterior axis specification axis specification lateral sprouting from an epithelium regulation of morphogenesis of an epithelium morphogenesis of an epithelial bud regulation of morphogenesis of a branching structure morphogenesis of an epithelial fold morphogenesis of embryonic epithelium prostatic bud formation regulation of prostatic bud formation regulation of animal organ formation embryonic digestive tract morphogenesis embryonic digestive tract development positive regulation of oligodendrocyte differentiation regulation of oligodendrocyte differentiation positive regulation of kidney smooth muscle cell differentiation branching involved in salivary gland morphogenesis regulation of neuroblast proliferation positive regulation of neuroblast proliferation regulation of glial cell proliferation glial cell proliferation roof of mouth development	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen organelle endoplasmic reticulum Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane extracellular region extracellular space cell surface cell periphery plasma membrane membrane microdomain membrane raft organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036844	Hint domain superfamily	Homologous Superfamily
A	IPR009045	Peptidase M74/Hedgehog-like, zinc-binding domain superfamily	Homologous Superfamily
A	IPR001657	Hedgehog protein	Family
A	IPR006141	Intein N-terminal splicing region	PTM
A	IPR003586	Hint domain C-terminal	Domain
A	IPR003587	Hint domain N-terminal	Domain
A	IPR000320	Hedgehog, N-terminal signalling domain	Domain
A	IPR001767	Hedgehog protein, Hint domain	Domain
A	IPR050387	Hedgehog Signaling	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q15465	holoprosencephaly holoprosencephaly 3 microphthalmia, isolated, with coloboma 5 polydactyly of a triphalangeal thumb solitary median maxillary central incisor syndrome microphthalmia Facial Dysmorphism with Multiple Malformations schizencephaly syndactyly type 4 familial schizencephaly polydactyly coloboma secondary Parkinson disease laurin-Sandrow syndrome nevoid basal cell carcinoma syndrome holoprosencephaly holoprosencephaly 3 microphthalmia, isolated, with coloboma 5 polydactyly of a triphalangeal thumb solitary median maxillary central incisor syndrome microphthalmia Facial Dysmorphism with Multiple Malformations schizencephaly syndactyly type 4 familial schizencephaly polydactyly coloboma secondary Parkinson disease laurin-Sandrow syndrome nevoid basal cell carcinoma syndrome alobar holoprosencephaly pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia brain disease coloboma, ocular, autosomal dominant semilobar holoprosencephaly Currarino triad tibia, hypoplasia or aplasia of, with polydactyly intellectual disability microphthalmia with coloboma 1 pancreatic intraductal papillary-mucinous carcinoma cancer congenital anomaly of kidney and urinary tract skin basal cell carcinoma triphalangeal thumb-polysyndactyly syndrome interstitial cystitis lobar holoprosencephaly pancreatic intraductal papillary-mucinous neoplasm hepatocellular carcinoma hypoplastic tibiae-postaxial polydactyly syndrome

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.