9YZM | pdb_00009yzm

Isoreticular co-crystal 1 with asymmetrical expanded duplex (31mer) containing insert sequence CTAATTAGGC and loaded with Even-skipped homeodomain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
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)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002854	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8002855	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Homeodomain-like	8057603	3000001	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Homeodomain-like	8057603	3000001	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D, E	PF00046	Homeodomain (Homeodomain)	Homeodomain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-
D, E	Segmentation protein even-skipped	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 transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription factor activity, RNA polymerase II-specific	developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation germ-band extension multicellular organism development anatomical structure morphogenesis anatomical structure development gastrulation with mouth forming first gastrulation involving germ band extension regulation of neuron projection development axonogenesis regulation of cellular component organization developmental process multicellular organismal process embryonic morphogenesis embryo development gastrulation germ-band extension multicellular organism development anatomical structure morphogenesis anatomical structure development gastrulation with mouth forming first gastrulation involving germ band extension regulation of neuron projection development axonogenesis regulation of cellular component organization regulation of cellular process cellular developmental process regulation of developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis regulation of axonogenesis cell differentiation cellular component organization or biogenesis regulation of anatomical structure morphogenesis system development regulation of biological process plasma membrane bounded cell projection organization regulation of cell projection organization biological regulation nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development cellular process regulation of plasma membrane bounded cell projection organization blastoderm segmentation embryonic pattern specification anterior/posterior pattern specification segmentation pattern specification process regionalization periodic partitioning periodic partitioning by pair rule gene motor neuron axon guidance axon guidance neuron projection guidance trunk segmentation heart development heart morphogenesis animal organ development circulatory system development animal organ morphogenesis 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 adult heart 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 head development head segmentation posterior head segmentation negative regulation of stem cell differentiation negative regulation of cell fate specification regulation of cardioblast cell fate specification regulation of cell differentiation negative regulation of cell fate commitment cardioblast cell fate commitment negative regulation of cardioblast cell fate specification regulation of cardioblast differentiation negative regulation of cardiac cell fate specification cardiac cell fate specification regulation of stem cell differentiation negative regulation of cell differentiation regulation of multicellular organismal process cardiac cell fate commitment negative regulation of cardiocyte differentiation negative regulation of cardioblast differentiation negative regulation of developmental process regulation of cell fate commitment cell fate specification cardiocyte differentiation cardioblast differentiation stem cell differentiation regulation of cell fate specification regulation of cardiocyte differentiation negative regulation of multicellular organismal process regulation of cardiac cell fate specification cardioblast cell fate specification cell fate commitment 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 anatomical structure formation involved in morphogenesis cephalic furrow formation regulation of syncytium formation by plasma membrane fusion cell-cell fusion muscle cell differentiation myotube differentiation muscle structure development syncytium formation myoblast fusion regulation of myoblast fusion syncytium formation by plasma membrane fusion striated muscle cell differentiation	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
B	DNA (31-MER)	-	-	-
A	DNA (31-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
D, E	IPR017970	Homeobox, conserved site	Conserved Site
D, E	IPR052002	Even-skipped homeobox domain-containing protein	Family
D, E	IPR009057	Homedomain-like superfamily	Homologous Superfamily
D, E	IPR020479	Homeodomain, metazoa	Domain
D, E	IPR001356	Homeodomain	Domain

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.