5T6B

X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form

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)
A	d5t6ba_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)
B	d5t6bb_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)
C	d5t6bc_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)
D	d5t6bd_	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	C-3'-methyltransferase-like	automated matches	(Actinomadura kijaniata ) [TaxId: 46161 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Zinc beta-ribbon	8051771	3001238	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zinc beta-ribbon	8051771	3001238	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zinc beta-ribbon	8051771	3001238	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CoA-binding Rossmann-fold domain	8051772	3000049	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8051770	3000118	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zinc beta-ribbon	8051771	3001238	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	PF08484	e5t6bA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08484	ECOD (1.6)
A	PF13489	e5t6bA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13489	ECOD (1.6)
A	PF08421	e5t6bA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF08421	ECOD (1.6)
B	PF08484	e5t6bB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08484	ECOD (1.6)
B	PF13489	e5t6bB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13489	ECOD (1.6)
B	PF08421	e5t6bB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF08421	ECOD (1.6)
C	PF08484	e5t6bC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08484	ECOD (1.6)
C	PF13489	e5t6bC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13489	ECOD (1.6)
C	PF08421	e5t6bC3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF08421	ECOD (1.6)
D	PF08484	e5t6bD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PF08484	ECOD (1.6)
D	PF13489	e5t6bD3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF13489	ECOD (1.6)
D	PF08421	e5t6bD2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF08421	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	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)
A	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	CATH (4.3.0)
C	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
C	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	6.20.50.110	Special	Other non-globular	N-terminal domain of TfIIb	Methyltransferase, zinc-binding domain	CATH (4.3.0)
D	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
D	6.10.250.3100	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF08421	Putative zinc binding domain (Methyltransf_13)	Putative zinc binding domain	This domain is found at the N-terminus of bacterial methyltransferases and contains four conserved cysteines suggesting a potential zinc binding domain.	Domain
A, B, C, D	PF08484	C-methyltransferase C-terminal domain (Methyltransf_14)	C-methyltransferase C-terminal domain	-	Family
A, B, C, D	PF13489	Methyltransferase domain (Methyltransf_23)	Methyltransferase domain	This family appears to be a methyltransferase domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Sugar 3-C-methyl transferase	cation binding ion binding binding metal ion binding small molecule binding transferase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013630	Methyltransferase putative zinc binding domain	Domain
A, B, C, D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A, B, C, D	IPR038576	Methyltransferase putative zinc binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR013691	C-methyltransferase	Domain

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.