4RYL | pdb_00004ryl

Human Protein Arginine Methyltransferase 3 in complex with 1-isoquinolin-6-yl-3-[2-oxo-2-(pyrrolidin-1-yl)ethyl]urea

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d4ryla_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Arginine methyltransferase	Protein arginine N-methyltransferase 3, PRMT3	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8041509	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Arginine methyltransferase C-terminal oligomerisation domain-like	8053431	3002184	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CBM_X2	e4rylA1	A: a/b three-layered sandwiches	X: Ribonuclease H-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: CBM_X2	ECOD (v294.1)
A	Amidase_2	e4rylA2	A: a/b three-layered sandwiches	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	2.70.160.11	Mainly Beta	Distorted Sandwich	Hnrnp arginine n-methyltransferase1	Hnrnp arginine n-methyltransferase1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22528	Arginine methyltransferase oligomerization subdomain (PRMT_C)	Arginine methyltransferase oligomerization subdomain	This entry represents a domain found C-terminal in protein arginine methyltransferases. This domain is involved in oligomerisation.	Domain
A	PF06325	Ribosomal protein L11 methyltransferase (PrmA) (PrmA)	Ribosomal protein L11 methyltransferase (PrmA)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PRMT3 protein	histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone methyltransferase activity histone H4R3 methyltransferase activity arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity histone modifying activity methyltransferase activity catalytic activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity protein-arginine N-methyltransferase activity histone methyltransferase activity histone H4R3 methyltransferase activity arginine N-methyltransferase activity protein methyltransferase activity N-methyltransferase activity histone modifying activity methyltransferase activity catalytic activity protein-arginine omega-N monomethyltransferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding protein-arginine omega-N asymmetric methyltransferase activity	regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization regulation of cellular process positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process cellular component organization or biogenesis positive regulation of cellular process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process regulation of biological process epigenetic regulation of gene expression biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process regulation of primary metabolic process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of DNA-templated transcription developmental process regulation of osteoblast differentiation multicellular organismal process cellular developmental process regulation of developmental process regulation of cell differentiation osteoblast differentiation positive regulation of developmental process positive regulation of osteoblast differentiation ossification positive regulation of cell differentiation cell differentiation negative regulation of post-translational protein modification regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process macromolecule modification post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal methylation diterpenoid metabolic process negative regulation of small molecule metabolic process oxoacid metabolic process regulation of lipid metabolic process organic acid biosynthetic process organic acid metabolic process terpenoid biosynthetic process negative regulation of lipid biosynthetic process carboxylic acid biosynthetic process regulation of small molecule metabolic process retinoic acid metabolic process small molecule metabolic process regulation of biological quality regulation of vitamin metabolic process regulation of hormone levels regulation of ketone metabolic process negative regulation of vitamin metabolic process retinoic acid biosynthetic process negative regulation of isoprenoid metabolic process regulation of isoprenoid metabolic process monocarboxylic acid metabolic process negative regulation of lipid metabolic process terpenoid metabolic process negative regulation of hormone metabolic process isoprenoid metabolic process regulation of hormone metabolic process ketone metabolic process lipid biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process isoprenoid biosynthetic process carboxylic acid metabolic process regulation of retinoic acid biosynthetic process hormone metabolic process vitamin metabolic process diterpenoid biosynthetic process negative regulation of retinoic acid biosynthetic process negative regulation of biosynthetic process retinoid metabolic process regulation of lipid biosynthetic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR049482	Protein arginine N-methyltransferase 3-like, C2H2 zinc finger domain	Domain
A	IPR025799	Protein arginine N-methyltransferase	Family
A	IPR013087	Zinc finger C2H2-type	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR036236	Zinc finger C2H2 superfamily	Homologous Superfamily
A	IPR055135	Protein arginine N-methyltransferase domain	Domain
A	IPR049009	Protein arginine N-methyltransferase 3, C2H2 zinc finger	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: O60678	atypical teratoid rhabdoid tumor lung cancer malignant glioma non-small cell lung carcinoma glioblastoma lung carcinoma malignant mesothelioma ovarian cancer large cell medulloblastoma malignant ependymoma nasopharyngeal carcinoma pituitary cancer

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.