7Q3O | pdb_00007q3o

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)
L [auth G]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
J [auth C]	SCOP2B Superfamily	Homeodomain-like	8070982	3000001	SCOP2B (2022-06-29)
I [auth K]	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)
L [auth G]	tRNA-synt_2	e7q3oG1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
K [auth E]	tRNA-synt_2	e7q3oE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
J [auth C]	tRNA-synt_2	e7q3oC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: tRNA-synt_2	ECOD (v294.1)
I [auth K]	tRNA-synt_2	e7q3oK1	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
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 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 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 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 digestive system development tube development digestive tract development anterior/posterior axis specification axis specification regulation of cellular process 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 embryonic pattern specification positive regulation of DNA-templated transcription positive regulation of biological process 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 cellular process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle chromatin chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle
B [auth H], D [auth I], F [auth J], H [auth L]	hydroxymethylated DNA (18-MER)	-	-	-
A, C [auth B], E [auth D], G [auth F]	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.