6QO4

Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from Mycobacterium abscessus in complex with Fragment 3 (2-(5-Isoxazolyl) phenol)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
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	d6qo4a_	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Mycobacteroides abscessus ) [TaxId: 36809 ],	SCOPe (2.08)
B	d6qo4b1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	automated matches	automated matches	(Mycobacteroides abscessus ) [TaxId: 36809 ],	SCOPe (2.08)
B	d6qo4b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacteroides abscessus ) [TaxId: 36809 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	alpha/beta knot	8066651	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8066651	3001122	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	PF01746	e6qo4A1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: PF01746	ECOD (1.6)
B	PF01746	e6qo4B1	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: PF01746	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01746	tRNA (Guanine-1)-methyltransferase (tRNA_m1G_MT)	tRNA (Guanine-1)-methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	tRNA (guanine-N(1)-)-methyltransferase	tRNA methyltransferase activity RNA methyltransferase activity tRNA (guanine(37)-N1)-methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid tRNA (guanine) methyltransferase activity catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity methyltransferase activity catalytic activity	methylation metabolic process cellular biosynthetic process cellular metabolic process tRNA modification RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification methylation metabolic process cellular biosynthetic process cellular metabolic process tRNA modification RNA metabolic process primary metabolic process gene expression macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process organic cyclic compound metabolic process RNA modification organic substance metabolic process biosynthetic process tRNA processing macromolecule modification organic substance biosynthetic process nucleic acid catabolic process cellular process macromolecule metabolic process RNA processing	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A, B	IPR016009	tRNA methyltransferase TRMD/TRM10-type domain	Domain
A, B	IPR023148	tRNA (guanine-N(1)-)-methyltransferase, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR002649	tRNA (guanine-N1-)-methyltransferase TrmD	Family

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 R01GM133198.