Annotations: 7YTA

crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth C]	Ribosomal_L2	e7ytaC1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.2)
C [auth B]	Ribosomal_L2	e7ytaB1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.2)
A	Ribosomal_L2	e7ytaA1	A: beta barrels	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B], E [auth C]	PF05641	Agenet domain (Agenet)	Agenet domain	This domain is related to the TUDOR domain Pfam:PF00567 [1]. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth P], D [auth Q], F [auth R]	H3(1-15)K9me2 peptide	DNA binding protein-containing complex binding binding chromatin binding nucleic acid binding nucleosome binding nucleosomal DNA binding chromatin DNA binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression regulation of cellular process negative regulation of biological process cellular component organization cellular component biogenesis cellular component assembly chromatin organization negative regulation of cellular process chromatin remodeling cellular component organization or biogenesis negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process heterochromatin formation epigenetic regulation of gene expression negative regulation of metabolic process biological regulation heterochromatin organization regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process cellular process negative regulation of gene expression, epigenetic regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle extracellular region membraneless organelle intracellular membraneless organelle chromocenter cytosol cell periphery plasma membrane membrane protein-containing complex protein-DNA complex nucleosome chromatin chromosome nucleus
A, C [auth B], E [auth C]	AGDP3 AGD1-2	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth P], D [auth Q], F [auth R]	IPR009072	Histone-fold	Homologous Superfamily
B [auth P], D [auth Q], F [auth R]	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
B [auth P], D [auth Q], F [auth R]	IPR000164	Histone H3/CENP-A	Family
A, C [auth B], E [auth C]	IPR007930	Protein of unknown function DUF724	Family
A, C [auth B], E [auth C]	IPR008395	Agenet-like domain	Domain
A, C [auth B], E [auth C]	IPR014002	Agenet domain, plant type	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B [auth P], D [auth Q], F [auth R]	MLY	Parent Component: LYS : AA0075 : N6,N6-dimethyl-L-lysine MOD:00084

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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.