9YZR | pdb_00009yzr

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence TAATTAGGCCG and loaded with ultrabithorax homeodomain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Homeodomain-like	8057619	3000001	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002855	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002854	3000034	SCOP2B (2022-06-29)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E	Homeotic protein ultrabithorax	protein binding binding protein domain specific binding DNA binding sequence-specific DNA 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 transcription factor binding protein binding binding protein domain specific binding DNA binding sequence-specific DNA 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 transcription factor binding transcription coregulator binding DNA-binding transcription factor activity, RNA polymerase II-specific transcription regulator activity DNA-binding transcription factor activity	regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation 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 negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process multicellular organismal process regulation of developmental process animal organ development positive regulation of biological process muscle structure development positive regulation of developmental process positive regulation of muscle organ development regulation of muscle organ development anatomical structure development positive regulation of multicellular organismal process regulation of multicellular organismal process muscle organ development heart development multicellular organism development circulatory system development system development digestive system development tube development midgut development digestive tract development blastoderm segmentation embryonic pattern specification specification of segmental identity, thorax segmentation pattern specification process embryo development regionalization specification of segmental identity, trunk trunk segmentation segment specification somatic muscle development respiratory system development open tracheal system development cellular developmental process regulation of cell fate commitment cell fate specification regulation of cell fate specification cell differentiation cell fate commitment Malpighian tubule development epithelium development tissue development renal system development anterior Malpighian tubule development renal tubule development regulation of growth regulation of developmental growth regulation of imaginal disc growth developmental growth growth imaginal disc growth imaginal disc development imaginal disc morphogenesis appendage development post-embryonic appendage morphogenesis leg disc development instar larval or pupal development metamorphosis leg disc morphogenesis imaginal disc-derived appendage morphogenesis anatomical structure morphogenesis appendage morphogenesis imaginal disc-derived appendage development instar larval or pupal morphogenesis post-embryonic animal morphogenesis post-embryonic development animal organ morphogenesis imaginal disc-derived leg morphogenesis haltere disc development haltere development cell fate determination cell fate commitment involved in pattern specification anterior/posterior pattern specification dorsal vessel aortic cell fate commitment cardiocyte differentiation embryonic heart tube anterior/posterior pattern specification cardiac cell fate commitment muscle cell fate specification muscle cell fate commitment muscle cell differentiation positive regulation of DNA-templated transcription 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 RNA metabolic process positive regulation of RNA biosynthetic process formation of primary germ layer embryonic morphogenesis gastrulation endoderm development anatomical structure formation involved in morphogenesis endoderm formation transcription by RNA polymerase II regulation of transcription by RNA polymerase II negative regulation of transcription by RNA polymerase II specification of animal organ identity animal organ formation mesodermal cell differentiation mesoderm morphogenesis mesodermal cell fate commitment mesoderm formation mesodermal cell fate specification mesoderm development cell fate commitment involved in formation of primary germ layer tissue morphogenesis	intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex transcription regulator complex transcription repressor complex protein-DNA complex intracellular organelle cellular anatomical structure intracellular anatomical structure organelle membraneless organelle intracellular membraneless organelle polytene chromosome chromosome chromosomal region polytene chromosome band protein-containing complex transcription regulator complex transcription repressor complex protein-DNA complex membrane-bounded organelle nucleus intracellular membrane-bounded organelle
C	Replication initiation protein	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding nucleic acid binding	cellular process plasmid maintenance nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication DNA replication initiation metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process	-
B	DNA (31-MER)	-	-	-
A	DNA (31-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E	IPR001827	Homeobox protein, antennapedia type, conserved site	Conserved Site
D, E	IPR017970	Homeobox, conserved site	Conserved Site
D, E	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D, E	IPR020479	Homeodomain, metazoa	Domain
D, E	IPR001356	Homeodomain	Domain
D, E	IPR050296	Antennapedia-type homeobox	Family
C	IPR000525	Initiator Rep protein, WH1 domain	Domain
C	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
C	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily

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.