5EF6 | pdb_00005ef6

Structure of HOXB13 complex with methylated DNA

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Homeodomain-like	8057595	3000001	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Homeodomain-like	8057595	3000001	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Homeodomain-like	8057595	3000001	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homeodomain-like	8057595	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)
J	Homeobox	e5ef6J1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
G	Homeobox	e5ef6G1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
D [auth B]	Homeobox	e5ef6B1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
A	Homeobox	e5ef6A1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
G	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
D [auth B]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B], G, J	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth F], F [auth E], I, L	DNA (5'-D(PGPGPAPCPCPTP(5CM)PGPTPAPAPAPAPCPAPCPAPA)-3')	-	-	-
B [auth C], E [auth D], H, K	DNA (5'-D(PTPTPGPTPGPTPTPTPTPAP(5CM)PGPAPGPGPTPCPC)-3')	-	-	-
A, D [auth B], G, J	Homeobox protein Hox-B13	DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor 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 transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription repressor activity, RNA polymerase II-specific DNA-binding transcription repressor 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	multicellular organismal process prostate gland development reproductive process gland development developmental process involved in reproduction prostate glandular acinus development prostate gland epithelium morphogenesis multicellular organism development gland morphogenesis anatomical structure development reproductive structure development animal organ morphogenesis system development developmental process multicellular organismal process prostate gland development reproductive process gland development developmental process involved in reproduction prostate glandular acinus development prostate gland epithelium morphogenesis multicellular organism development gland morphogenesis anatomical structure development reproductive structure development animal organ morphogenesis system development developmental process epithelium development reproductive system development animal organ development morphogenesis of an epithelium urogenital system development tissue development prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis prostate glandular acinus morphogenesis prostate gland morphogenesis tissue morphogenesis anatomical structure morphogenesis morphogenesis of a branching structure branching involved in prostate gland morphogenesis morphogenesis of a branching epithelium blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development response to stimulus response to stress response to wounding response to ketone response to lipid response to chemical response to oxygen-containing compound response to testosterone regulation of growth regulation of biological process biological regulation growth 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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process epidermis 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 epithelial cell maturation involved in prostate gland development cellular developmental process cell development epithelial cell differentiation cell differentiation cell maturation epithelial cell differentiation involved in prostate gland development developmental maturation epithelial cell development anatomical structure maturation epithelial cell maturation	protein-containing complex transcription regulator complex 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 protein-containing complex transcription regulator complex 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D [auth B], G, J	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, D [auth B], G, J	IPR017970	Homeobox, conserved site	Conserved Site
A, D [auth B], G, J	IPR001356	Homeodomain	Domain
A, D [auth B], G, J	IPR022067	Homeobox protein Hox1A3 N-terminal	Domain
A, D [auth B], G, J	IPR051003	Anterior-posterior axis regulatory homeobox	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, D [auth B], G, J	Pharos: Q92826	prostate cancer melanoma breast cancer breast carcinoma Neoplasm Invasiveness atypical teratoid rhabdoid tumor Crohn disease interstitial cystitis osteosarcoma prostate cancer, hereditary, 9 psoriasis cutaneous melanoma prostate carcinoma restless legs syndrome familial prostate carcinoma

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.