7Q3O

Structure of CDX1 bound to hydroxymethylated DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family 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)
I [auth K]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
J [auth C]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
L [auth G]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	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)
I [auth K]	PF00046	e7q3oK1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
J [auth C]	PF00046	e7q3oC1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
K [auth E]	PF00046	e7q3oE1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)
L [auth G]	PF00046	e7q3oG1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF00046	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth K], J [auth C], K [auth E], L [auth G]	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth K], J [auth C], K [auth E], L [auth G]	Homeobox protein CDX-1	DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding organic cyclic compound 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 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 binding double-stranded DNA binding organic cyclic compound 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 transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific nucleoside phosphate binding nucleotide binding heterocyclic compound binding methyl-CpG binding small molecule binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	developmental process multicellular organismal process animal organ development multicellular organism development anatomical structure morphogenesis skeletal system development anatomical structure development skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development system development cellular developmental process cell differentiation developmental process multicellular organismal process animal organ development multicellular organism development anatomical structure morphogenesis skeletal system development anatomical structure development skeletal system morphogenesis animal organ morphogenesis bone morphogenesis bone development system development cellular developmental process cell differentiation cellular process somitogenesis regulation of developmental process chordate embryonic development segmentation anterior/posterior pattern specification pattern specification process embryo 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 anterior/posterior axis specification axis specification regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process cellular metabolic process primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of DNA-templated transcription positive regulation of biological process positive regulation of cellular metabolic process positive regulation of biosynthetic process positive regulation of cellular process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process	intracellular organelle protein-containing complex intracellular anatomical structure protein-DNA complex organelle intracellular non-membrane-bounded organelle chromatin chromosome cellular anatomical entity non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle
A, C [auth B], E [auth D], G [auth F]	hydroxymethylated DNA (18-MER)	-	-	-
B [auth H], D [auth I], F [auth J], H [auth L]	hydroxymethylated DNA (18-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [auth K], J [auth C], K [auth E], L [auth G]	Pharos: P47902	colorectal cancer ulcerative colitis osteosarcoma 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 R01GM133198.