1YFL | pdb_00001yfl

T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base

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)
H [auth E]	d1yfle1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N6 adenine-specific DNA methylase, DAM	DNA methylase T4DAM	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
G [auth D]	d1yfld1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N6 adenine-specific DNA methylase, DAM	DNA methylase T4DAM	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
F [auth B]	d1yflb1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N6 adenine-specific DNA methylase, DAM	DNA methylase T4DAM	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
E [auth A]	d1yfla1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	N6 adenine-specific DNA methylase, DAM	DNA methylase T4DAM	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H [auth E]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034341	3000118	SCOP2B (2022-06-29)
G [auth D]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034341	3000118	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034341	3000118	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8034341	3000118	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)
H [auth E]	CMAS, Methyltransf_25	e1yflE1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: CMAS, Methyltransf_25	ECOD (v294.1)
G [auth D]	CMAS, Methyltransf_25	e1yflD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: CMAS, Methyltransf_25	ECOD (v294.1)
F [auth B]	CMAS, Methyltransf_25	e1yflB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: CMAS, Methyltransf_25	ECOD (v294.1)
E [auth A]	CMAS, Methyltransf_25	e1yflA1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: CMAS, Methyltransf_25	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth E]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
H [auth E]	1.10.1020.10	Mainly Alpha	Orthogonal Bundle	Adenine-specific Methyltransferase	domain 2	CATH (4.3.0)
G [auth D]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
G [auth D]	1.10.1020.10	Mainly Alpha	Orthogonal Bundle	Adenine-specific Methyltransferase	domain 2	CATH (4.3.0)
F [auth B]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
F [auth B]	1.10.1020.10	Mainly Alpha	Orthogonal Bundle	Adenine-specific Methyltransferase	domain 2	CATH (4.3.0)
E [auth A]	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
E [auth A]	1.10.1020.10	Mainly Alpha	Orthogonal Bundle	Adenine-specific Methyltransferase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth A], F [auth B], G [auth D], H [auth E]	PF02086	D12 class N6 adenine-specific DNA methyltransferase (MethyltransfD12)	D12 class N6 adenine-specific DNA methyltransferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth A], F [auth B], G [auth D], H [auth E]	DNA adenine methylase	DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity cation binding binding ion binding S-adenosyl-L-methionine binding sulfur compound binding DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity methyltransferase activity S-adenosylmethionine-dependent methyltransferase activity catalytic activity cation binding binding ion binding S-adenosyl-L-methionine binding sulfur compound binding small molecule binding sequence-specific DNA binding DNA binding nucleic acid binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair methylation biological process involved in interspecies interaction between organisms response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus DNA modification defense response to other organism macromolecule modification response to external biotic stimulus symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated evasion of recognition by host innate immune effector symbiont-mediated response to host defenses symbiont-mediated evasion of host innate immune response symbiont-mediated evasion of host restriction-modification system response to host immune response symbiont-mediated evasion of host immune response response to host	-
A [auth F], B [auth G], C [auth H], D [auth I]	5'-D(PTPCPAPCPAPGPGPAPTPCPCPTPGPTPGPA)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth D], H [auth E]	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
E [auth A], F [auth B], G [auth D], H [auth E]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
E [auth A], F [auth B], G [auth D], H [auth E]	IPR012327	D12 class N6 adenine-specific DNA methyltransferase	Family
E [auth A], F [auth B], G [auth D], H [auth E]	IPR023095	Adenine-specific methyltransferase, domain 2	Homologous Superfamily
E [auth A], F [auth B], G [auth D], H [auth E]	IPR012263	Adenine modification methylase, M.EcoRV-type	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.