3RKQ

NKX2.5 Homeodomain dimer bound to ANF-242 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-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3rkqa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Homeodomain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3rkqa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rkqb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Homeodomain-like	Homeodomain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3rkqb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2B Superfamily	Homeodomain-like	8071006	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8071006	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)
A	Homeobox	e3rkqA1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Homeobox	ECOD (1.6)
B	Homeobox	e3rkqB1	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)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
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
A, B	PF00046	Homeodomain (Homeodomain)	Homeodomain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Homeobox protein Nkx-2.5	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 DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator 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 DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific DNA-binding transcription activator activity transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding protein binding DNA-binding transcription factor 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 chromatin binding identical protein binding protein homodimerization activity protein dimerization activity	heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation heart process multicellular organismal process system process regulation of biological process regulation of cardiac conduction regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation cardiac conduction regulation of multicellular organismal process heart contraction blood circulation developmental process heart development multicellular organism development anatomical structure development animal organ development circulatory system development system development cardiac chamber morphogenesis heart morphogenesis ventricular septum development anatomical structure morphogenesis cardiac septum development cardiac septum morphogenesis ventricular septum morphogenesis cardiac chamber development animal organ morphogenesis cardiac ventricle development epithelium development embryonic heart tube left/right pattern formation tube development pattern specification process embryo development tissue development embryonic heart tube development regionalization embryonic organ development left/right pattern formation heart growth cell population proliferation developmental growth cardiac muscle tissue development cardiac muscle cell proliferation growth organ growth striated muscle tissue development muscle cell proliferation cellular process cardiac muscle tissue growth muscle tissue development striated muscle cell proliferation regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic 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 regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cellular response to stimulus response to stimulus signaling negative regulation of signaling regulation of canonical Wnt signaling pathway canonical Wnt signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cell communication cell communication negative regulation of Wnt signaling pathway negative regulation of cellular process signal transduction Wnt signaling pathway regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway negative regulation of response to stimulus negative regulation of signal transduction negative regulation of canonical Wnt signaling pathway regulation of response to stimulus regulation of cell communication apoptotic process involved in heart morphogenesis apoptotic process involved in morphogenesis cell death apoptotic process involved in development apoptotic process programmed cell death cellular developmental process cell differentiation epithelial cell differentiation hemopoiesis cell development embryo development ending in birth or egg hatching pharyngeal system development chordate embryonic development outflow tract septum morphogenesis outflow tract morphogenesis immune system development spleen development immune system process hematopoietic or lymphoid organ development 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 regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription negative regulation of cardiac muscle cell apoptotic process muscle cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of cardiac muscle cell apoptotic process regulation of muscle cell apoptotic process regulation of programmed cell death cardiac muscle cell apoptotic process negative regulation of apoptotic process regulation of striated muscle cell apoptotic process striated muscle cell apoptotic process negative regulation of muscle cell apoptotic process negative regulation of striated muscle cell apoptotic process cardiac muscle cell development muscle cell differentiation cardiac pacemaker cell development muscle structure development striated muscle cell development muscle cell development atrioventricular node development atrioventricular node cell development cardiac cell development cardiac conduction system development atrioventricular node cell differentiation cardiac muscle cell differentiation cardiocyte differentiation striated muscle cell differentiation cardiac pacemaker cell differentiation cardiac septum cell differentiation Purkinje myocyte development ventricular cardiac muscle tissue development Purkinje myocyte differentiation His-Purkinje system development His-Purkinje system cell differentiation adult heart development negative regulation of cellular metabolic process negative regulation of RNA biosynthetic process transcription by RNA polymerase II negative regulation of nucleobase-containing compound metabolic process negative regulation of macromolecule metabolic process regulation of transcription by RNA polymerase II negative regulation of DNA-templated transcription negative regulation of transcription by RNA polymerase II negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of RNA metabolic process positive regulation of blood circulation positive regulation of heart contraction positive regulation of multicellular organismal process positive regulation of DNA-templated transcription 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 RNA biosynthetic process regulation of epithelial cell apoptotic process epithelial cell apoptotic process negative regulation of epithelial cell apoptotic process tube morphogenesis embryonic heart tube morphogenesis heart looping determination of bilateral symmetry epithelial tube morphogenesis determination of left/right symmetry specification of symmetry embryonic organ morphogenesis embryonic morphogenesis morphogenesis of an epithelium determination of heart left/right asymmetry tissue morphogenesis ventricular cardiac muscle tissue morphogenesis ventricular trabecula myocardium morphogenesis muscle organ development muscle tissue morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis heart trabecula morphogenesis trabecula morphogenesis muscle organ morphogenesis regulation of developmental process regulation of cell differentiation positive regulation of developmental process regulation of cardioblast differentiation positive regulation of cell differentiation positive regulation of cardiocyte differentiation regulation of stem cell differentiation positive regulation of cardioblast differentiation positive regulation of stem cell differentiation cardioblast differentiation stem cell differentiation regulation of cardiocyte differentiation bundle of His development cardiac muscle cell fate commitment muscle cell fate commitment cardiac cell fate commitment cardiac pacemaker cell fate commitment atrioventricular node cell fate commitment cell fate commitment cardiac atrium morphogenesis cardiac atrium development atrial septum morphogenesis atrial septum development thyroid gland development endocrine system development gland development atrial cardiac muscle cell differentiation atrial cardiac muscle cell development proepicardium development mesenchyme development septum transversum development positive regulation of cell population proliferation positive regulation of epithelial cell proliferation regulation of cell population proliferation regulation of epithelial cell proliferation epithelial cell proliferation heart trabecula formation anatomical structure formation involved in morphogenesis trabecula formation negative regulation of muscle cell differentiation regulation of striated muscle cell differentiation myotube differentiation negative regulation of myotube differentiation regulation of myotube differentiation negative regulation of cell differentiation negative regulation of developmental process negative regulation of striated muscle cell differentiation regulation of muscle cell differentiation regulation of cardiac muscle contraction cardiac muscle contraction muscle contraction muscle system process regulation of muscle system process striated muscle contraction regulation of striated muscle contraction regulation of muscle contraction septum secundum development heart valve development aortic valve development heart valve morphogenesis semi-lunar valve development aortic valve morphogenesis regulation of DNA-templated transcription initiation transcription initiation at RNA polymerase II promoter positive regulation of DNA-templated transcription initiation positive regulation of transcription initiation by RNA polymerase II DNA-templated transcription initiation regulation of transcription initiation by RNA polymerase II ventricular cardiac muscle cell differentiation ventricular cardiac muscle cell development cellular component assembly involved in morphogenesis non-membrane-bounded organelle assembly cellular component organization cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly actin filament-based process cellular component organization or biogenesis actomyosin structure organization actin cytoskeleton organization organelle assembly ventricular cardiac myofibril assembly myofibril assembly organelle organization cardiac myofibril assembly supramolecular fiber organization cytoskeleton organization venous blood vessel development pulmonary myocardium development vasculature development blood vessel development positive regulation of neuron differentiation neurogenesis neuron differentiation nervous system development generation of neurons regulation of neuron differentiation blood vessel morphogenesis vasculogenesis regulation of localization transport regulation of transport regulation of monoatomic ion transport regulation of sodium ion transport establishment of localization metal ion transport positive regulation of sodium ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport monoatomic cation transport regulation of metal ion transport sodium ion transport atrial cardiac muscle tissue development regulation of growth regulation of cardiac muscle tissue growth regulation of organ growth regulation of heart growth regulation of cardiac muscle cell proliferation regulation of multicellular organismal development regulation of developmental growth cardiac ventricle formation cardiac chamber formation right ventricular cardiac muscle tissue morphogenesis cardiac right ventricle morphogenesis	protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus protein-containing complex transcription regulator complex intracellular anatomical structure cytoplasm cellular anatomical entity intracellular organelle organelle intracellular non-membrane-bounded organelle chromatin chromosome non-membrane-bounded organelle RNA polymerase II transcription regulator complex membrane-bounded organelle nucleus nuclear protein-containing complex intracellular membrane-bounded organelle Nkx-2.5 complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen protein-DNA complex
C	ANF-242 DNA	-	-	-
D	ANF-242 DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR020479	Homeodomain, metazoa	Domain
A, B	IPR001356	Homeodomain	Domain
A, B	IPR050394	Homeobox NK-like transcription regulators	Family
A, B	IPR017970	Homeobox, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P52952	tetralogy of fallot hypoplastic left heart syndrome hypothyroidism, congenital, nongoitrous, 5 atrial fibrillation atrial septal defect 7 congenital hypothyroidism conotruncal heart malformations double outlet right ventricle ventricular septal defect 3 hypoplastic left heart syndrome 2 ventricular septal defect familial atrial fibrillation Cardiomegaly dilated cardiomyopathy myotonic dystrophy type 1 tetralogy of fallot hypoplastic left heart syndrome hypothyroidism, congenital, nongoitrous, 5 atrial fibrillation atrial septal defect 7 congenital hypothyroidism conotruncal heart malformations double outlet right ventricle ventricular septal defect 3 hypoplastic left heart syndrome 2 ventricular septal defect familial atrial fibrillation Cardiomegaly dilated cardiomyopathy myotonic dystrophy type 1 aortic valve disease 1 atrial fibrillation, familial, 1 myotonic dystrophy osteosarcoma congenital myotonic dystrophy thyroid ectopia familial isolated congenital asplenia Holt-Oram syndrome aortic valve calcification athyreosis intellectual disability atrial septal defect progressive familial heart block, type 1A dilated cardiomyopathy 1A heart disease hypertrophic pyloric stenosis aortic valve disease hypothyroidism open-angle glaucoma cerebrovascular disorder right atrial isomerism

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.