5XOD | pdb_00005xod

Crystal structure of human Smad2-Ski complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5xoda1	All beta proteins	SMAD/FHA domain	SMAD/FHA domain	SMAD domain	Smad2 MH2 domain	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5xoda2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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	SCOP2B Superfamily	SMAD/FHA domain-like	8038261	3000137	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	MH2	e5xodA1	A: beta sandwiches	X: SMAD/FHA domain (From Topology)	H: SMAD/FHA domain (From Topology)	T: SMAD/FHA domain	F: MH2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.200.10	Mainly Beta	Sandwich	Tumour Suppressor Smad4		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03166	MH2 domain (MH2)	MH2 domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	Ski oncogene	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity enzyme regulator activity molecular function inhibitor activity histone deacetylase inhibitor activity molecular function regulator activity enzyme inhibitor activity histone deacetylase regulator activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity enzyme regulator activity molecular function inhibitor activity histone deacetylase inhibitor activity molecular function regulator activity enzyme inhibitor activity histone deacetylase regulator activity ubiquitin protein ligase binding protein binding binding ubiquitin-like protein ligase binding enzyme binding identical protein binding protein domain specific binding DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor activity DNA binding sequence-specific DNA binding double-stranded DNA binding nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding transcription regulatory region nucleic acid binding RNA polymerase II cis-regulatory region sequence-specific DNA binding kinase binding protein kinase binding SMAD binding transcription factor binding DNA-binding transcription factor binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding cellular response to stimulus activin receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process response to stimulus signaling negative regulation of signaling regulation of molecular function positive regulation of molecular function regulation of DNA binding regulation of binding biological regulation positive regulation of binding positive regulation of DNA binding cellular response to stimulus activin receptor signaling pathway cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process response to stimulus signaling negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of activin receptor signaling pathway negative regulation of cellular process signal transduction enzyme-linked receptor protein signaling pathway regulation of biological process regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication cellular process transforming growth factor beta receptor superfamily signaling pathway regulation of activin receptor signaling pathway negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway developmental process multicellular organismal process heart development heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth animal organ development organ growth tissue development striated muscle tissue development circulatory system development multicellular organism development anatomical structure development muscle cell proliferation cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation system development cellular developmental process peripheral nervous system axon ensheathment peripheral nervous system development cell development nervous system development glial cell development myelination neurogenesis Schwann cell development gliogenesis axon ensheathment ensheathment of neurons glial cell differentiation cell differentiation myelination in peripheral nervous system Schwann cell differentiation sensory organ development eye development retina development in camera-type eye visual system development camera-type eye development sensory system development cellular response to growth factor stimulus negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway cellular response to endogenous stimulus BMP signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway response to endogenous stimulus regulation of cellular response to growth factor stimulus response to BMP response to growth factor muscle structure development striated muscle cell differentiation muscle cell differentiation myotube differentiation negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette SMAD protein signal transduction regulation of SMAD protein signal transduction negative regulation of SMAD protein signal transduction embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure negative regulation of transforming growth factor beta receptor signaling pathway cellular response to transforming growth factor beta stimulus regulation of transforming growth factor beta receptor signaling pathway regulation of cellular response to transforming growth factor beta stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process positive regulation of response to stimulus positive regulation of Wnt signaling pathway Wnt signaling pathway positive regulation of cellular process regulation of Wnt signaling pathway positive regulation of signaling camera-type eye morphogenesis eye morphogenesis sensory organ morphogenesis animal organ morphogenesis negative regulation of cell population proliferation fibroblast proliferation regulation of fibroblast proliferation regulation of cell population proliferation negative regulation of fibroblast proliferation somatic stem cell population maintenance maintenance of cell number stem cell population maintenance cell motility 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 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 transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process head development olfactory lobe development forebrain development brain development central nervous system development olfactory bulb development telencephalon development skeletal system development skeletal system morphogenesis bone morphogenesis bone development nose morphogenesis nose development respiratory system development myotube cell development skeletal muscle fiber development skeletal muscle tissue development skeletal muscle organ development striated muscle cell development muscle cell development muscle organ development face morphogenesis head morphogenesis face development body morphogenesis regulation of osteoblast differentiation regulation of developmental process negative regulation of osteoblast differentiation negative regulation of developmental process regulation of cell differentiation osteoblast differentiation ossification negative regulation of cell differentiation limb development appendage development embryonic limb morphogenesis embryonic appendage morphogenesis appendage morphogenesis limb morphogenesis regulation of neurogenesis regulation of gliogenesis negative regulation of glial cell proliferation regulation of cell development negative regulation of Schwann cell proliferation regulation of nervous system development negative regulation of neurogenesis regulation of glial cell proliferation regulation of multicellular organismal process negative regulation of nervous system development Schwann cell proliferation regulation of multicellular organismal development regulation of Schwann cell proliferation negative regulation of gliogenesis negative regulation of cell development glial cell proliferation negative regulation of multicellular organismal process anterior/posterior axis specification anterior/posterior pattern specification pattern specification process axis specification regionalization lens morphogenesis in camera-type eye lens development in camera-type eye roof of mouth development	protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle protein-containing complex transcription regulator complex cellular anatomical structure intracellular anatomical structure cytoplasm intracellular organelle centrosome microtubule organizing center cytoskeleton organelle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen transcription repressor complex nuclear body PML body
A	Mothers against decapentaplegic homolog 2	SMAD binding protein binding binding R-SMAD binding transforming growth factor beta receptor binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding co-SMAD binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding SMAD binding protein binding binding R-SMAD binding transforming growth factor beta receptor binding signaling receptor binding type I transforming growth factor beta receptor binding cytokine receptor binding co-SMAD binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding nucleic acid binding cis-regulatory region sequence-specific DNA binding transcription regulatory region nucleic acid binding cytoskeletal protein binding tau protein binding I-SMAD binding phosphatase binding enzyme binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity cation binding ion binding metal ion binding small molecule binding identical protein binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding DNA-binding transcription factor binding RNA polymerase II transcription regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding chromatin binding disordered domain specific binding protein domain specific binding	developmental process multicellular organismal process digestive system development foregut morphogenesis tube development embryonic morphogenesis embryo development digestive tract development multicellular organism development anatomical structure morphogenesis tube morphogenesis embryonic foregut morphogenesis digestive tract morphogenesis anatomical structure development developmental process multicellular organismal process digestive system development foregut morphogenesis tube development embryonic morphogenesis embryo development digestive tract development multicellular organism development anatomical structure morphogenesis tube morphogenesis embryonic foregut morphogenesis digestive tract morphogenesis anatomical structure development system development mesoderm morphogenesis mesenchyme morphogenesis animal organ development mesenchyme development tissue development tissue morphogenesis paraxial mesoderm development animal organ morphogenesis paraxial mesoderm morphogenesis mesoderm development regulation of biosynthetic process regulation of biological process regulation of cellular process biological regulation positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process embryonic pattern specification dorsal/ventral axis specification pattern specification process regionalization embryonic axis specification dorsal/ventral pattern formation zygotic specification of dorsal/ventral axis axis specification cell population proliferation response to sterol response to stimulus response to lipid response to alcohol response to chemical response to oxygen-containing compound response to cholesterol RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process embryo development ending in birth or egg hatching chordate embryonic development in utero embryonic development regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription secondary palate development roof of mouth development cellular developmental process cell differentiation cell fate commitment regulation of developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation negative regulation of cellular process negative regulation of cell differentiation positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process establishment of protein localization nitrogen compound transport transport signaling hormone secretion cell communication protein localization to extracellular region peptide secretion localization secretion by cell amide transport signal release regulation of biological quality intracellular protein localization secretion regulation of hormone levels establishment of protein localization to extracellular region cell-cell signaling export from cell protein secretion establishment of localization peptide transport protein transport peptide hormone secretion macromolecule localization hormone transport insulin secretion cellular response to stimulus cellular response to growth factor stimulus cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway cellular response to transforming growth factor beta stimulus response to endogenous stimulus cellular response to endogenous stimulus response to transforming growth factor beta transforming growth factor beta receptor signaling pathway response to growth factor transforming growth factor beta receptor superfamily signaling pathway signal transduction enzyme-linked receptor protein signaling pathway trophoblast cell migration multi-multicellular organism process reproductive process ameboidal-type cell migration cell migration cell motility female pregnancy embryo implantation multi-organism reproductive process formation of primary germ layer gastrulation anatomical structure formation involved in morphogenesis mesoderm formation negative regulation of RNA biosynthetic process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process heart development epithelium development circulatory system development pericardium development activin receptor signaling pathway nodal signaling pathway developmental growth growth organ growth regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction regulation of transforming growth factor beta receptor signaling pathway regulation of signaling regulation of cellular response to transforming growth factor beta stimulus regulation of cellular response to growth factor stimulus regulation of response to stimulus regulation of cell communication regulation of epithelial to mesenchymal transition positive regulation of epithelial to mesenchymal transition positive regulation of developmental process positive regulation of cell differentiation regulation of multicellular organismal process epithelial to mesenchymal transition positive regulation of multicellular organismal process mesenchymal cell differentiation embryonic organ morphogenesis embryonic cranial skeleton morphogenesis skeletal system development cranial skeletal system development embryonic skeletal system development skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis respiratory tube development lung development respiratory system development response to hexose response to monosaccharide response to carbohydrate response to glucose positive regulation of cell communication positive regulation of signal transduction positive regulation of BMP signaling pathway positive regulation of response to stimulus BMP signaling pathway cellular response to BMP stimulus regulation of BMP signaling pathway positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway response to BMP positive regulation of signaling heart valve development aortic valve development heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis ureteric bud development mesonephric epithelium development kidney epithelium development mesonephros development renal system development kidney development mesonephric tubule development pancreas development endocardial cushion morphogenesis heart morphogenesis endocardial cushion development pulmonary valve morphogenesis pulmonary valve development intracellular signal transduction SMAD protein signal transduction intracellular signaling cassette RNA processing regulatory ncRNA processing regulatory ncRNA-mediated gene silencing primary miRNA processing negative regulation of gene expression miRNA processing endoderm development endoderm formation epithelial cell differentiation neuroepithelial cell differentiation odontoblast differentiation columnar/cuboidal epithelial cell differentiation lateral mesoderm development determination of left/right asymmetry in lateral mesoderm determination of bilateral symmetry determination of left/right symmetry left/right pattern formation specification of symmetry ossification negative regulation of multicellular organismal process regulation of ossification negative regulation of ossification post-embryonic development anterior/posterior pattern specification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle activin responsive factor complex intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex transcription regulator complex RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle activin responsive factor complex intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromatin chromosome heteromeric SMAD protein complex SMAD protein complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen homomeric SMAD protein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
B	IPR047315	Ski oncogene-like, Dachshund-homology domain	Domain
B	IPR010919	SAND-like domain superfamily	Homologous Superfamily
B	IPR023216	Transcription regulator SKI/SnoN	Family
B	IPR037000	Ski-like, DNA-binding domain superfamily	Homologous Superfamily
B	IPR003380	SKI/SNO/DAC domain	Domain
B	IPR014890	c-SKI SMAD4-binding domain	Domain
A	IPR036578	SMAD MH1 domain superfamily	Homologous Superfamily
A	IPR017855	SMAD-like domain superfamily	Homologous Superfamily
A	IPR013019	MAD homology, MH1	Domain
A	IPR013790	Dwarfin	Family
A	IPR003619	MAD homology 1, Dwarfin-type	Domain
A	IPR008984	SMAD/FHA domain superfamily	Homologous Superfamily
A	IPR001132	SMAD domain, Dwarfin-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P12755	chromosome 1p36 deletion syndrome Shprintzen-Goldberg syndrome craniosynostosis Craniofacial Abnormalities neural tube defect aortic aneurysm iniencephaly juvenile dermatomyositis neurenteric cyst pancreatic intraductal papillary-mucinous carcinoma arthrogryposis Pick disease diastematomyelia tuberculosis heart disease chromosome 1p36 deletion syndrome Shprintzen-Goldberg syndrome craniosynostosis Craniofacial Abnormalities neural tube defect aortic aneurysm iniencephaly juvenile dermatomyositis neurenteric cyst pancreatic intraductal papillary-mucinous carcinoma arthrogryposis Pick disease diastematomyelia tuberculosis heart disease intellectual disability large cell medulloblastoma ovarian cancer acute myeloid leukemia pancreatic intraductal papillary-mucinous neoplasm astrocytic tumor psoriasis craniorachischisis tethered spinal cord syndrome Ehlers-Danlos syndrome gastric carcinoma hydrocephalus invasive ductal breast carcinoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia cancer rheumatoid arthritis thoracic aortic aneurysm Emery-Dreifuss muscular dystrophy head and neck cancer
A	Pharos: Q15796	Liver Cirrhosis, Experimental acromicric dysplasia lymphoplasmacytic lymphoma ovarian cancer primitive neuroectodermal tumor subependymal giant cell astrocytoma cancer colorectal cancer connective tissue disease hepatitis kidney disease lung cancer Marfan syndrome pituitary cancer psoriasis Liver Cirrhosis, Experimental acromicric dysplasia lymphoplasmacytic lymphoma ovarian cancer primitive neuroectodermal tumor subependymal giant cell astrocytoma cancer colorectal cancer connective tissue disease hepatitis kidney disease lung cancer Marfan syndrome pituitary cancer psoriasis amyotrophic lateral sclerosis thoracic aortic aneurysm colorectal carcinoma dermatomyositis lung disease medulloblastoma plasma cell myeloma right atrial isomerism breast cancer geleophysic dysplasia holoprosencephaly

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.