2HVR | pdb_00002hvr

Structure of T4 RNA Ligase 2 with Nicked 5'-Adenylated nucleic acid duplex containing a 3'-deoxyribonucleotide at the nick

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth A]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8041405	3000798	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8041405	3000798	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)
G [auth A]	RNA_lig_RNL2	e2hvrA2	A: alpha bundles	X: Spectrin repeat-like	H: Alpha-hemoglobin stabilizing protein AHSP (From Topology)	T: Alpha-hemoglobin stabilizing protein AHSP	F: RNA_lig_RNL2	ECOD (1.6)
G [auth A]	RNA_ligase	e2hvrA1	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: RNA_ligase	ECOD (1.6)
H [auth B]	RNA_lig_RNL2	e2hvrB3	A: alpha bundles	X: Spectrin repeat-like	H: Alpha-hemoglobin stabilizing protein AHSP (From Topology)	T: Alpha-hemoglobin stabilizing protein AHSP	F: RNA_lig_RNL2	ECOD (1.6)
H [auth B]	RNA_ligase	e2hvrB2	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: RNA_ligase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth A]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
G [auth A]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
G [auth A]	1.10.10.1810	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	RNA ligase	CATH (4.3.0)
H [auth B]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
H [auth B]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
H [auth B]	1.10.10.1810	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	RNA ligase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B]	PF09414	RNA ligase (RNA_ligase)	RNA ligase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], D [auth F]	5'-D(APTPTPCPCPGPAPTPAPGPTPGPGPGPGPTPCPGPCPAPAPTPTPG)-3'	-	-	-
B [auth D], E [auth G]	5'-D(CPAPAPTPTPGPCPGPAPC)-R(P(OMC)PC)-3'	-	-	-
C [auth E], F [auth H]	5'-R(PA)-D(PCPAPCPTPAPTPCPGPGPAPAP*T)-3'	-	-	-
G [auth A], H [auth B]	T4 RNA ligase 2	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide 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 RNA ligase (ATP) activity catalytic activity, acting on RNA RNA ligase activity catalytic activity, acting on a nucleic acid catalytic activity ligase activity cation binding metal ion binding	nucleobase-containing compound metabolic process RNA metabolic process metabolic process cellular process primary metabolic process macromolecule metabolic process RNA repair nucleic acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B]	IPR041948	RNA ligase 1/2, C-terminal domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR044263	RNA ligase 2, viral	Family
G [auth A], H [auth B]	IPR012647	RNA ligase, Rnl2	Family
G [auth A], H [auth B]	IPR040609	RNA ligase 2, C-terminal	Domain
G [auth A], H [auth B]	IPR021122	RNA ligase domain, REL/Rln2	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 R01GM157729.