Annotations: 8YDD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8071014	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	WD40 repeat-like	8098826	3001694	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	WD40 repeat-like	8098826	3001694	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	WD40 repeat-like	8098826	3001694	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, E	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain
A, B, C	PF00400	WD domain, G-beta repeat (WD40)	WD domain, G-beta repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E	Homeobox protein NANOG	DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding DNA-binding transcription factor activity, RNA polymerase II-specific DNA-binding transcription repressor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding RNA polymerase II transcription regulatory region sequence-specific DNA binding cis-regulatory region sequence-specific DNA binding RNA polymerase II cis-regulatory region sequence-specific DNA binding RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity protein-macromolecule adaptor activity molecular adaptor activity chromatin binding transcription factor binding protein binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity identical protein binding	cellular response to stimulus cellular response to nitrogen compound response to ketone response to stimulus response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to ether cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to ether response to chemical response to rapamycin cellular response to stimulus cellular response to nitrogen compound response to ketone response to stimulus response to alcohol response to oxygen-containing compound response to nitrogen compound cellular response to ether cellular response to oxygen-containing compound cellular response to chemical stimulus cellular response to alcohol response to ether response to chemical response to rapamycin cellular process cellular response to rapamycin cellular response to ketone cellular response to BMP stimulus regulation of biological process cell surface receptor protein serine/threonine kinase signaling pathway regulation of cellular process cellular response to growth factor stimulus cell surface receptor signaling pathway signaling response to endogenous stimulus biological regulation cell communication cellular response to endogenous stimulus response to BMP transforming growth factor beta receptor superfamily signaling pathway signal transduction response to growth factor BMP signaling pathway enzyme-linked receptor protein signaling pathway negative regulation of stem cell differentiation developmental process cellular developmental process regulation of developmental process negative regulation of developmental process negative regulation of biological process regulation of cell differentiation stem cell differentiation cell differentiation regulation of stem cell differentiation negative regulation of cellular process negative regulation of cell differentiation multicellular organismal process negative regulation of cell fate specification endodermal cell fate specification embryo development negative regulation of cell fate commitment multicellular organism development regulation of endodermal cell differentiation anatomical structure development formation of primary germ layer regulation of endodermal cell fate specification regulation of cell fate commitment embryonic morphogenesis cell fate specification tissue development gastrulation cell fate commitment involved in formation of primary germ layer anatomical structure morphogenesis negative regulation of endodermal cell differentiation negative regulation of endodermal cell fate specification endoderm development regulation of cell fate specification anatomical structure formation involved in morphogenesis endoderm formation cell fate commitment endodermal cell fate commitment endodermal cell differentiation tissue regeneration developmental growth growth regeneration response to peptide cellular response to erythropoietin response to cytokine cellular response to cytokine stimulus response to erythropoietin response to retinoic acid response to lipid negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication regulation of signaling regulation of BMP signaling pathway negative regulation of response to stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction regulation of response to stimulus regulation of cell communication negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction development of primary sexual characteristics reproductive structure development system development cell growth multidimensional cell growth mesodermal cell differentiation mesoderm morphogenesis tissue morphogenesis mesodermal cell fate commitment mesoderm formation mesoderm development cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process maintenance of cell number stem cell population maintenance cell dedifferentiation dedifferentiation positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of metabolic process stem cell division regulation of stem cell division cell division regulation of cell division somatic stem cell population maintenance negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of cell cycle mitotic cell cycle regulation of mitotic cell cycle positive regulation of mitotic cell cycle cell cycle regulation of cell cycle embryonic pattern specification pattern specification process positive regulation of transcription by RNA polymerase II	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen membraneless organelle intracellular membraneless organelle chromatin chromosome
A, B, C	WD repeat-containing protein 5	histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity histone H3Q5ser reader activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone reader activity histone H3 reader activity chromatin-protein adaptor activity histone H3K4me3 reader activity protein-macromolecule adaptor activity molecular adaptor activity histone H3Q5ser reader activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H3K4 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity histone H3K4me1 reader activity	monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process monosaccharide metabolic process regulation of cellular process positive regulation of biological process gluconeogenesis regulation of primary metabolic process positive regulation of metabolic process regulation of small molecule metabolic process positive regulation of biosynthetic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process positive regulation of cellular process positive regulation of gluconeogenesis regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process positive regulation of glucose metabolic process biosynthetic process regulation of gluconeogenesis metabolic process cellular process positive regulation of carbohydrate metabolic process regulation of carbohydrate biosynthetic process positive regulation of small molecule metabolic process regulation of metabolic process glucose metabolic process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process macromolecule metabolic process developmental process multicellular organism development multicellular organismal process skeletal system development anatomical structure development system development regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription positive regulation of DNA-templated transcription positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process cell division regulation of cell division regulation of embryonic development regulation of multicellular organismal development regulation of developmental process embryo development regulation of multicellular organismal process regulation of transcription by RNA polymerase II cell cycle regulation of cell cycle negative regulation of biological process negative regulation of RNA biosynthetic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process	protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex protein-containing complex intracellular anatomical structure catalytic complex intracellular membraneless organelle chromatin chromosome transferase complex histone acetyltransferase complex acetyltransferase complex intracellular organelle cellular anatomical structure organelle membraneless organelle protein acetyltransferase complex intracellular protein-containing complex membrane-bounded organelle histone methyltransferase complex nucleus membrane-enclosed lumen nuclear protein-containing complex intracellular membrane-bounded organelle intracellular organelle lumen nucleoplasm organelle lumen methyltransferase complex nuclear lumen Set1C/COMPASS complex mitotic spindle cytoskeleton spindle microtubule cytoskeleton MLL3/4 complex NSL complex H4 histone acetyltransferase complex ATAC complex SAGA-type complex MLL1/2 complex MLL1 complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E	IPR017970	Homeobox, conserved site	Conserved Site
D, E	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D, E	IPR050460	Distal-less homeobox transcription factors	Family
D, E	IPR001356	Homeodomain	Domain
A, B, C	IPR019775	WD40 repeat, conserved site	Conserved Site
A, B, C	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
A, B, C	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B, C	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
A, B, C	IPR001680	WD40 repeat	Repeat

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.