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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
B	SCOP2B Superfamily	alpha/beta knot	8040017	3001122	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	Stap_Strp_toxin	e1k3rB1	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Stap_Strp_toxin	ECOD (v294.1)
B	RecU	e1k3rB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: RecU	ECOD (v294.1)
A	Methyltrn_RNA_3	e1k3rA2	A: a/b three-layered sandwiches	X: alpha/beta knot	H: alpha/beta knot	T: alpha/beta knot	F: Methyltrn_RNA_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.