Annotations: 3GDE

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF04679	e3gdeA2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF04679	ECOD (1.6)
A	PF04675	e3gdeA7	A: alpha bundles	X: ATP-dependent DNA ligase DNA-binding domain (From Topology)	H: ATP-dependent DNA ligase DNA-binding domain (From Topology)	T: ATP-dependent DNA ligase DNA-binding domain	F: PF04675	ECOD (1.6)
A	PF01068	e3gdeA5	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: PF01068	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3260.10	Mainly Alpha	Orthogonal Bundle	DNA ligase i, domain 1	DNA ligase, ATP-dependent, N-terminal domain	CATH (4.3.0)
A	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	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	PF04675	DNA ligase N terminus (DNA_ligase_A_N)	DNA ligase N terminus	-	Family
A	PF01068	ATP dependent DNA ligase domain (DNA_ligase_A_M)	ATP dependent DNA ligase domain	This domain belongs to a more diverse superfamily, including Pfam:PF01331 and Pfam:PF01653 [3].	Domain
A	PF04679	ATP dependent DNA ligase C terminal region (DNA_ligase_A_C)	ATP dependent DNA ligase C terminal region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA ligase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding ligase activity, forming phosphoric ester bonds DNA ligase (ATP) activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity cation binding metal ion binding	cellular process cell cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process nucleobase-containing compound biosynthetic process cellular process cell cycle nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular biosynthetic process cellular metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process DNA biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair cell division DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A	IPR000977	DNA ligase, ATP-dependent	Family
A	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
A	IPR022865	DNA ligase, ATP-dependent, bacterial/archaeal	Family
A	IPR012310	DNA ligase, ATP-dependent, central	Domain
A	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR012309	DNA ligase, ATP-dependent, C-terminal	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.