1PUF

Crystal Structure of HoxA9 and Pbx1 homeodomains bound to DNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth A]	d1pufa_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Homeodomain	Homeobox protein hox-a9	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth B]	d1pufb_	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Homeodomain	pbx1	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth A]	SCOP2 Family	Homeodomain	8002358	4000291	SCOP2 (2022-06-29)
C [auth A]	SCOP2 Superfamily	Homeodomain-like	8057596	3000001	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Family	Homeodomain	8002359	4000291	SCOP2 (2022-06-29)
D [auth B]	SCOP2 Superfamily	Homeodomain-like	8057597	3000001	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth A]	Homeobox	e1pufA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
D [auth B]	Homeobox_KN	e1pufB1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox_KN	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth A]	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain
D [auth B]	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	5'-D(APCPTPCPTPAPTPGPAPTPTPTPAPCPGPAPCPGPCPT)-3'	-	-	-
B [auth E]	5'-D(TPAPGPCPGPTPCPGPTPAPAPAPTPCPAPTPAPGPAPG)-3'	-	-	-
C [auth A]	Homeobox protein Hox-A9	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 organic cyclic compound binding transcription regulatory region nucleic acid 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 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 organic cyclic compound binding transcription regulatory region nucleic acid 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 transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity protein binding enzyme binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development spermatogenesis sexual reproduction multicellular organismal reproductive process male gamete generation gamete generation limb development appendage development embryonic forelimb morphogenesis embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development anatomical structure morphogenesis forelimb morphogenesis appendage morphogenesis limb morphogenesis prostate gland development gland development urogenital system development response to organic substance response to ketone response to lipid response to stimulus response to chemical response to oxygen-containing compound response to testosterone response to organic cyclic compound regulation of biosynthetic process regulation of biological process regulation of cellular process cellular biosynthetic process cellular metabolic process biological regulation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression organic substance metabolic process biosynthetic process organic substance biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process fertilization single fertilization mammary gland development embryonic organ morphogenesis chordate embryonic development embryo development ending in birth or egg hatching skeletal system development animal organ morphogenesis embryonic skeletal system development skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic cyclic compound biosynthetic process uterus development regulation of developmental process cellular developmental process negative regulation of biological process cell development regulation of cell differentiation regulation of cell development cell differentiation negative regulation of cellular process negative regulation of cell differentiation regulation of immune system process regulation of multicellular organismal process regulation of multicellular organismal development negative regulation of developmental process hemopoiesis regulation of myeloid cell differentiation negative regulation of myeloid cell differentiation myeloid cell differentiation immune system process regulation of hemopoiesis definitive hemopoiesis regulation of primary metabolic process 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 DNA-templated transcription 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 anterior/posterior pattern specification pattern specification process regionalization proximal/distal pattern formation endothelial cell activation cell activation	protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
D [auth B]	Pre-B-cell leukemia transcription factor-1	transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region 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 transcription factor binding transcription coregulator binding transcription corepressor binding protein binding binding DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region 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 DNA-binding transcription factor binding DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity	multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation anatomical structure development negative regulation of cellular process negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation head development central nervous system development animal organ development brain development cellular biosynthetic process negative regulation of DNA-binding transcription factor activity 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 organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process cellular metabolic process negative regulation of molecular function 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 regulation of molecular function organic cyclic compound metabolic process regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process immune system development gland development hematopoietic or lymphoid organ development thymus development immune system process anatomical structure morphogenesis animal organ morphogenesis steroid metabolic process lipid biosynthetic process steroid biosynthetic process lipid metabolic process ossification regulation of multicellular organismal process regulation of ossification urogenital system development regulation of stem cell proliferation cell population proliferation positive regulation of cell population proliferation positive regulation of biological process positive regulation of stem cell proliferation stem cell proliferation regulation of cell population proliferation positive regulation of cellular process limb development appendage development embryonic limb morphogenesis embryonic morphogenesis embryonic appendage morphogenesis embryo development appendage morphogenesis limb morphogenesis embryonic organ development hemopoiesis cell development embryonic hemopoiesis spleen development adrenal gland development endocrine system development reproductive process sex differentiation developmental process involved in reproduction embryo development ending in birth or egg hatching skeletal system development chordate embryonic development embryonic skeletal system development sensory organ development eye development visual system development sensory system development transcription by RNA polymerase II regulation of transcription by RNA polymerase II cell activation mononuclear cell differentiation natural killer cell activation lymphocyte differentiation lymphocyte activation leukocyte activation natural killer cell differentiation leukocyte differentiation mesonephric epithelium development kidney epithelium development nephron morphogenesis branching morphogenesis of an epithelial tube nephron tubule morphogenesis nephron epithelium morphogenesis nephron tubule development renal system development ureteric bud morphogenesis tube morphogenesis branching involved in ureteric bud morphogenesis renal tubule development epithelial tube morphogenesis nephron development nephron epithelium development ureteric bud development epithelium development tube development mesonephros development morphogenesis of an epithelium tissue development tissue morphogenesis kidney morphogenesis morphogenesis of a branching structure mesonephric tubule morphogenesis kidney development mesonephric tubule development renal tubule morphogenesis morphogenesis of a branching epithelium cell cycle G2/M phase transition mitotic cell cycle process G2/M transition of mitotic cell cycle cell cycle phase transition cell cycle mitotic cell cycle cell cycle process mitotic cell cycle phase transition 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 cellular metabolic process positive regulation of biosynthetic process positive regulation of RNA biosynthetic process positive regulation of cellular biosynthetic process anterior/posterior pattern specification pattern specification process regionalization neuron development regulation of cell cycle phase transition regulation of mitotic cell cycle positive regulation of mitotic cell cycle phase transition positive regulation of cell cycle process positive regulation of mitotic cell cycle regulation of cell cycle positive regulation of G2/M transition of mitotic cell cycle regulation of G2/M transition of mitotic cell cycle regulation of cell cycle process regulation of cell cycle G2/M phase transition positive regulation of cell cycle G2/M phase transition positive regulation of cell cycle regulation of mitotic cell cycle phase transition positive regulation of cell cycle phase transition proximal/distal pattern formation	RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen RNA polymerase II transcription regulator complex membrane-bounded organelle protein-containing complex intracellular anatomical structure nucleus nuclear protein-containing complex transcription regulator complex intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle organelle cytoplasm membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR001356	Homeobox domain	Domain
C [auth A]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
C [auth A]	IPR017970	Homeobox, conserved site	Conserved Site
C [auth A]	IPR006711	Hox9, N-terminal activation domain	Domain
C [auth A]	IPR017112	Homeobox protein HXA9/HXB9/HXC9	Family
C [auth A]	IPR020479	Homeobox domain, metazoa	Domain
D [auth B]	IPR001356	Homeobox domain	Domain
D [auth B]	IPR009057	Homeobox-like domain superfamily	Homologous Superfamily
D [auth B]	IPR017970	Homeobox, conserved site	Conserved Site
D [auth B]	IPR005542	PBX, PBC domain	Domain
D [auth B]	IPR008422	Homeobox KN domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth B]	Pharos: P40424	Burkitt lymphoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm Organic Mental Disorders, Substance-Induced pancreatic ductal adenocarcinoma acute lymphoblastic leukemia breast cancer substance-related disorder cancer cystic fibrosis hematologic disease lung adenocarcinoma malignant glioma medulloblastoma Burkitt lymphoma interstitial cystitis malignant colon neoplasm malignant pancreatic neoplasm Organic Mental Disorders, Substance-Induced pancreatic ductal adenocarcinoma acute lymphoblastic leukemia breast cancer substance-related disorder cancer cystic fibrosis hematologic disease lung adenocarcinoma malignant glioma medulloblastoma osteosarcoma pancreatic intraductal papillary-mucinous carcinoma acute myeloid leukemia attention deficit hyperactivity disorder, inattentive type substance dependence breast carcinoma congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay intellectual disability lung cancer malignant mesothelioma non-small cell lung carcinoma ovarian cancer pituitary cancer adrenal cortex carcinoma substance abuse ulcerative colitis congenital anomaly of kidney and urinary tract drug dependence glioblastoma

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.