6DT1

Crystal structure of the ligase from bacteriophage T4 complexed with DNA intermediate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e6dt1A1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
A	F_UNCLASSIFIED	e6dt1A3	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: F_UNCLASSIFIED	ECOD (1.6)
A	PF01068	e6dt1A2	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)
B [auth E]	F_UNCLASSIFIED	e6dt1E2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: F_UNCLASSIFIED	ECOD (1.6)
B [auth E]	F_UNCLASSIFIED	e6dt1E1	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: F_UNCLASSIFIED	ECOD (1.6)
B [auth E]	PF01068	e6dt1E3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth E]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth E]	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 ligase activity, forming phosphoric ester bonds catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid catalytic activity DNA ligase activity ligase activity cation binding metal ion binding DNA ligase (ATP) activity	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 response to stimulus response to stimulus cellular response to stress DNA damage response response to stress 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 response to stimulus response to stimulus cellular response to stress DNA damage response response to stress cellular process DNA repair DNA recombination	-
C [auth B], F	DNA (5'-D(GPCPTPGPAPTPGPCPGPTP*(DOC))-3')	-	-	-
D [auth C], G	DNA (5'-D((AMP)GPTPCPGPGPAPCPTPGPAP*)-3')	-	-	-
E [auth D], H	DNA (5'-D(TPCPAPGPTPCPCPGPAPCPGPAPCPGPCPAPTPCPAPGP*C)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth E]	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A, B [auth E]	IPR012310	DNA ligase, ATP-dependent, central	Domain
A, B [auth E]	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 R01GM133198.