5TWK | pdb_00005twk

Crystal Structure of RlmH in Complex with Sinefungin

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth D]	d5twkd1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B [auth D]	d5twkd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d5twka1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C [auth A]	d5twka2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d5twkb1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D [auth B]	d5twkb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A [auth C]	d5twkc1	Alpha and beta proteins (a/b)	alpha/beta knot	alpha/beta knot	YbeA-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A [auth C]	d5twkc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth D]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	alpha/beta knot	8043915	3001122	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	alpha/beta knot	8043915	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)
B [auth D]		e5twkD1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F:	ECOD (develop294)
C [auth A]		e5twkA1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F:	ECOD (develop294)
D [auth B]		e5twkB1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F:	ECOD (develop294)
A [auth C]		e5twkC1	A: alpha bundles	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F:	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
C [auth A]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
D [auth B]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)
A [auth C]	3.40.1280.10	Alpha Beta	3-Layer(aba) Sandwich	Alpha/beta knot	SPOUT methyltransferase, trefoil knot domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], B [auth D], C [auth A], D [auth B]	PF02590	Predicted SPOUT methyltransferase (SPOUT_MTase)	Predicted SPOUT methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D], C [auth A], D [auth B]	Ribosomal RNA large subunit methyltransferase H	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA methyltransferase activity rRNA methyltransferase activity rRNA (pseudouridine-N3-)-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 identical protein binding protein binding binding protein homodimerization activity protein dimerization activity RNA methyltransferase activity rRNA methyltransferase activity rRNA (pseudouridine-N3-)-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 rRNA (pseudouridine) methyltransferase activity methyltransferase activity catalytic activity ribonucleoprotein complex binding protein-containing complex binding ribosome binding	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 rRNA base methylation RNA methylation	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D], C [auth A], D [auth B]	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal	Homologous Superfamily
A [auth C], B [auth D], C [auth A], D [auth B]	IPR029028	Alpha/beta knot methyltransferases	Homologous Superfamily
A [auth C], B [auth D], C [auth A], D [auth B]	IPR003742	RNA methyltransferase RlmH	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.