5ZWX | pdb_00005zwx

Crystal structure of Raphanus sativus AGDP1 AGD12 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)
C [auth B]	UNK_F_TYPE	e5zwxB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: UNK_F_TYPE	ECOD (1.6)
A	UNK_F_TYPE	e5zwxA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	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]	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
A, C [auth B]	DUF724 domain-containing protein 6-like	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

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

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.