1K3R | pdb_00001k3r

Crystal Structure of the Methyltransferase with a Knot from Methanobacterium thermoautotrophicum

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family 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	d1k3ra1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Hypothetical protein MTH1 (MT0001), insert domain	Hypothetical protein MTH1 (MT0001), insert domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
A	d1k3ra2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	Hypothetical protein MTH1 (MT0001), dimerisation domain	Hypothetical protein MTH1 (MT0001), dimerisation domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
B	d1k3rb1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Hypothetical protein MTH1 (MT0001), insert domain	Hypothetical protein MTH1 (MT0001), insert domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)
B	d1k3rb2	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	Hypothetical protein MTH1 (MT0001), dimerisation domain	Hypothetical protein MTH1 (MT0001), dimerisation domain	(Methanothermobacter thermautotrophicus ) [TaxId: 145262 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Hypothetical protein MTH1 (MT0001), insert domain	8027636	4002180	SCOP2 (2022-06-29)
A	SCOP2 Family	Hypothetical protein MTH1 (MT0001), dimerisation domain	8027638	4002344	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleic acid-binding proteins	8040015	3000135	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha/beta knot	8040017	3001122	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	alpha/beta knot	8040017	3001122	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8040015	3000135	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	Methyltrn_RNA_3_2nd	e1k3rA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Methyltrn_RNA_3_2nd	ECOD (1.6)
A	Methyltrn_RNA_3_1st	e1k3rA2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: Methyltrn_RNA_3_1st	ECOD (1.6)
B	Methyltrn_RNA_3_2nd	e1k3rB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Methyltrn_RNA_3_2nd	ECOD (1.6)
B	Methyltrn_RNA_3_1st	e1k3rB2	A: a/b three-layered sandwiches	X: alpha/beta knot (From Topology)	H: alpha/beta knot (From Topology)	T: alpha/beta knot	F: Methyltrn_RNA_3_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
B	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02598	Putative RNA methyltransferase (Methyltrn_RNA_3)	Putative RNA methyltransferase	-	Family

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003750	Putative RNA methyltransferase C9orf114-like	Family
A, B	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A, B	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A, B	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

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.