3EGV

Ribosomal protein L11 methyltransferase (PrmA) in complex with trimethylated ribosomal protein L11

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3egva1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Ribosomal protein L11 methyltransferase PrmA	PrmA-like protein TTHA0656 (TT0836)	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d3egvb1	Alpha and beta proteins (a+b)	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal L11/L12e N-terminal domain	Ribosomal protein L11, N-terminal domain	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Ribosomal protein L11 methyltransferase PrmA	8028672	4001159	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8041051	3000118	SCOP2 (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	prmA_like	e3egvA2	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain (From Topology)	T: Ribosomal protein L11 methyltransferase PrmA N-terminal ferredoxin-like domain	F: prmA_like	ECOD (1.6)
A	Methyltransf_11_4	e3egvA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_4	ECOD (1.6)
B	Ribosomal_L11_N	e3egvB1	A: a+b two layers	X: Ribosomal protein L11/L12e N-terminal domain-like	H: Ribosomal protein L11/L12e N-terminal domain (From Topology)	T: Ribosomal protein L11/L12e N-terminal domain	F: Ribosomal_L11_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.70.1170	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Sun protein	CATH (4.3.0)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.30.1550.10	Alpha Beta	2-Layer Sandwich	Ribosomal protein L11, N-terminal domain	Ribosomal protein L11/L12, N-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF06325	Ribosomal protein L11 methyltransferase (PrmA) (PrmA)	Ribosomal protein L11 methyltransferase (PrmA)	-	Family
B	PF03946	Ribosomal protein L11, N-terminal domain (Ribosomal_L11_N)	Ribosomal protein L11, N-terminal domain	The N-terminal domain of Ribosomal protein L11 adopts an alpha/beta fold and is followed by the RNA binding C-terminal domain.	Domain
B	PF00298	Ribosomal protein L11, RNA binding domain (Ribosomal_L11)	Ribosomal protein L11, RNA binding domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Ribosomal protein L11 methyltransferase	catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity histone modifying activity transferase activity methyltransferase activity catalytic activity histone methyltransferase activity	methylation metabolic process cellular process	cellular anatomical structure intracellular anatomical structure cytoplasm
B	50S ribosomal protein L11	structural molecule activity structural constituent of ribosome RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR050078	Ribosomal protein L11 methyltransferase PrmA	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR004498	Ribosomal protein L11 methyltransferase	Family
B	IPR020785	Large ribosomal subunit protein uL11, conserved site	Conserved Site
B	IPR020783	Large ribosomal subunit protein uL11, C-terminal	Domain
B	IPR000911	Ribosomal protein uL11	Family
B	IPR036769	Large ribosomal subunit protein uL11, C-terminal domain superfamily	Homologous Superfamily
B	IPR006519	Large ribosomal subunit protein uL11, bacterial-type	Family
B	IPR020784	Large ribosomal subunit protein uL11, N-terminal	Domain
B	IPR036796	Large ribosomal subunit protein uL11, N-terminal domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
B	4MM	Parent Component: MET RESID: AA0456 PSI-MOD : N,N,N-trimethyl-L-methionine MOD:01382

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.