7YTA | pdb_00007yta

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: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.1)
C [auth B]	Ribosomal_L2	e7ytaB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.1)
A	Ribosomal_L2	e7ytaA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: Ribosomal_L2	ECOD (v294.1)

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
A, C [auth B], E [auth C]	AGDP3 AGD1-2	-	-	-
B [auth P], D [auth Q], F [auth R]	H3(1-15)K9me2 peptide	DNA binding binding nucleic acid binding protein heterodimerization activity protein binding protein dimerization activity structural molecule activity structural constituent of chromatin	-	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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

Protein Modification Annotation

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

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.