5VAH | pdb_00005vah

Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	DNAG_N	e5vahB1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)
A	DNAG_N	e5vahA1	A: a/b three-layered sandwiches	X: Spectrin repeat-like	H: Spectrin repeat	T: Spectrin repeat	F: DNAG_N	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)
A	2.170.270.10	Mainly Beta	Beta Complex	Beta-clip-like	SET domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00856	SET domain (SET)	SET domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Histone H3.2	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, B	Probable Histone-lysine N-methyltransferase ATXR5	protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K27 methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity histone H3K27 monomethyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H3 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone H3K27 methyltransferase activity histone methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity histone H3K27 monomethyltransferase activity catalytic activity transcription regulator activity transcription coregulator activity protein-macromolecule adaptor activity molecular adaptor activity protein-lysine-acetyltransferase activity protein N-acetyltransferase activity acyltransferase activity N-acetyltransferase activity protein N-acyltransferase activity histone acetyltransferase activity acetyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups N-acyltransferase activity chromatin binding binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of biological process regulation of cellular process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological process regulation of cellular process biological regulation primary metabolic process DNA metabolic process regulation of macromolecule metabolic process nucleic acid metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of metabolic process regulation of DNA replication regulation of DNA metabolic process methylation RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II regulation of RNA biosynthetic process regulation of transcription by RNA polymerase II regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription cell cycle regulation of cell cycle	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle chloroplast membraneless organelle intracellular membraneless organelle chromatin chromosome nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR009072	Histone-fold	Homologous Superfamily
C, D	IPR007125	Core Histone H2A/H2B/H3 domain	Domain
C, D	IPR000164	Histone H3/CENP-A	Family
A, B	IPR001965	Zinc finger, PHD-type	Domain
A, B	IPR046341	SET domain superfamily	Homologous Superfamily
A, B	IPR001214	SET domain	Domain
A, B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
A, B	IPR053114	Histone-lysine N-methyltransferase ATXR5/ATXR6	Family
A, B	IPR019787	Zinc finger, PHD-finger	Domain
A, B	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
A, B	IPR019786	Zinc finger, PHD-type, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	DA2	Parent Component: ARG RESID: AA0068 PSI-MOD : asymmetric dimethyl-L-arginine MOD:00077

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.

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