3GRV | pdb_00003grv

Crystal Structure of the Complex between Adenosine and Methanocaldococcus jannaschi Dim1

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3grva_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	automated matches	automated matches	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	rRNA adenine dimethylase, catalytic domain-like	8089263	4003608	SCOP2 (2022-06-29)
A	SCOP2 Family	rRNA adenine dimethylase, C-terminal domain-like	8090723	4007710	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8089264	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S13-like H2TH domain	8090724	3000053	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	RrnaAD	e3grvA1	A: alpha bundles	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: RrnaAD	ECOD (develop294)

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	1.10.8.100	Mainly Alpha	Orthogonal Bundle	Helicase, Ruva Protein	domain 3	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Dimethyladenosine transferase	RNA binding binding nucleic acid binding RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity N-methyltransferase activity methyltransferase activity RNA binding binding nucleic acid binding RNA methyltransferase activity rRNA (adenine-N6,N6-)-dimethyltransferase activity rRNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity catalytic activity, acting on a rRNA S-adenosylmethionine-dependent methyltransferase activity N-methyltransferase activity methyltransferase activity rRNA (adenine) methyltransferase activity catalytic activity	ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process ribonucleoprotein complex biogenesis rRNA methylation RNA metabolic process rRNA processing rRNA modification nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process ribosome biogenesis nucleic acid biosynthetic process cellular component organization or biogenesis RNA processing rRNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001737	Ribosomal RNA adenine methyltransferase KsgA/Erm	Family
A	IPR020598	Ribosomal RNA adenine methylase transferase, N-terminal	Domain
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR023165	rRNA adenine dimethylase-like, C-terminal	Homologous Superfamily
A	IPR011530	Ribosomal RNA adenine dimethylase	Family
A	IPR020596	Ribosomal RNA adenine methylase transferase, conserved site	Conserved Site

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.