7Q4N | pdb_00007q4n

transcription factor CDX2 bound to hydroxymethylated DNA

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F [auth C]	tRNA-synt_2	e7q4nC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
C [auth K]	tRNA-synt_2	e7q4nK1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth K], F [auth C]	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth K], F [auth C]	Homeobox protein CDX-2	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 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 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 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 nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding	developmental process cellular developmental process cell differentiation cellular process cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell developmental process cellular developmental process cell differentiation cellular process cellular localization transport endosome to lysosome transport intracellular transport lysosomal transport establishment of localization vesicle-mediated transport localization intercellular transport establishment of localization in cell vacuolar transport anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis somitogenesis multicellular organismal process regulation of developmental process chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo development multicellular organism development embryo development ending in birth or egg hatching somite development regulation of multicellular organismal process regulation of somitogenesis regulation of anatomical structure morphogenesis epithelium development regulation of biological process biological regulation tissue development regionalization anatomical structure formation involved in morphogenesis placenta development labyrinthine layer development in utero embryonic development embryonic placenta development embryonic organ development digestive system development intestinal epithelial cell differentiation tube development digestive tract development epithelial cell differentiation columnar/cuboidal epithelial cell differentiation system development regulation of cellular process positive regulation of biological process regulation of cell differentiation positive regulation of developmental process positive regulation of cell differentiation positive regulation of cellular process trophectodermal cell differentiation blastocyst formation blastocyst development anterior/posterior axis specification axis specification cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation somatic stem cell population maintenance maintenance of cell number stem cell population maintenance RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic 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 metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process vasculature development blood vessel development circulatory system development 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 embryonic pattern specification stem cell differentiation 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 establishment or maintenance of bipolar cell polarity establishment or maintenance of epithelial cell apical/basal polarity establishment or maintenance of apical/basal cell polarity establishment or maintenance of cell polarity	membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membrane-bounded organelle condensed nuclear chromosome intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle nuclear chromosome chromosome intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle condensed chromosome nuclear lumen nucleoplasm chromatin protein-containing complex transcription regulator complex transcription repressor complex
B [auth D], E	DNA (18-MER)	-	-	-
A, D [auth B]	DNA (18-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth K], F [auth C]	IPR017970	Homeobox, conserved site	Conserved Site
C [auth K], F [auth C]	IPR009057	Homedomain-like superfamily	Homologous Superfamily
C [auth K], F [auth C]	IPR006820	Caudal-like activation domain	Domain
C [auth K], F [auth C]	IPR000047	Helix-turn-helix motif	Conserved Site
C [auth K], F [auth C]	IPR020479	Homeodomain, metazoa	Domain
C [auth K], F [auth C]	IPR001356	Homeodomain	Domain
C [auth K], F [auth C]	IPR047152	Caudal homeobox	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth K], F [auth C]	Pharos: Q99626	cancer Hashimoto thyroiditis ulcerative colitis digestive system disease hypothyroidism exocrine pancreatic carcinoma psoriasis

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.