5CCB | pdb_00005ccb

Crystal structure of human m1A58 methyltransferase in a complex with tRNA3Lys and SAH

External Resource: Annotation

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: 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	8089458	3000118	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transcription elongation factor, GreA/GreB-like	8090639	3002449	SCOP2B (2022-06-29)
B	SCOP2 Family	tRNA (1-methyladenosine)-methyltransferase non-catalytic subunit, TRM6-like	8045534	4004521	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8090619	3000118	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Transcription elongation factor, GreA/GreB-like	8090670	3002449	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	PapD_N	e5ccbA1	A: alpha bundles	X: P-loop domains-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PapD_N	ECOD (develop294)
B	Gcd10p	e5ccbB1	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: Gcd10p	ECOD (develop294)
B	E1_FCCH	e5ccbB2	A: alpha bundles	X: Transmembrane heme-binding four-helical bundle	H: Anticodon-binding domain of Class II aaRS	T: Anticodon-binding domain of Class II aaRS	F: E1_FCCH	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.330.20	Alpha Beta	Roll	Vcp-like ATPase	Chain A, domain 2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF08704	tRNA methyltransferase complex GCD14 subunit (GCD14)	tRNA methyltransferase complex GCD14 subunit	-	Family
B	PF04189	Gcd10p family (Gcd10p)	Gcd10p family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A	tRNA methyltransferase activity RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA transferase activity S-adenosylmethionine-dependent methyltransferase activity tRNA (adenine) methyltransferase activity tRNA (adenine(58)-N1)-methyltransferase activity methyltransferase activity catalytic activity mRNA (adenine-N1-)-methyltransferase activity mRNA methyltransferase activity	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation mRNA processing mRNA metabolic process	protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
B	tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6	RNA binding binding nucleic acid binding	RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing RNA processing tRNA modification primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process macromolecule methylation tRNA metabolic process RNA modification biosynthetic process methylation macromolecule modification metabolic process cellular process macromolecule metabolic process RNA methylation tRNA methylation mRNA processing mRNA metabolic process	protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle protein-containing complex tRNA (m1A) methyltransferase complex intracellular anatomical structure cellular anatomical structure catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
C [auth N]	tRNA3Lys	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR014816	tRNA (1-methyladenosine) methyltransferase catalytic subunit Gcd14	Family
A	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A	IPR049470	tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61, C-terminal	Domain
B	IPR017423	tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q96FX7	attention deficit hyperactivity disorder, inattentive type endogenous depression autism spectrum disorder heart disease bipolar disorder
B	Pharos: Q9UJA5	astrocytic tumor uterine corpus leiomyoma medulloblastoma ovarian 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.