7SX5 | pdb_00007sx5

Crystal structure of ligase I with nick duplexes containing mismatch A:C

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleic acid-binding proteins	8043720	3000135	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ATP-dependent DNA ligase DNA-binding domain	8043718	3001985	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8043722	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)
A	DNA_ligase_A_C	e7sx5A4	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: DNA_ligase_A_C	ECOD (1.6)
A	DNA_ligase_A_N	e7sx5A2	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: DNA_ligase_A_N	ECOD (1.6)
A	DNA_ligase_A_M	e7sx5A3	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: DNA_ligase_A_M	ECOD (1.6)

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	This region is found in many but not all ATP-dependent DNA ligase enzymes (EC:6.5.1.1). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA ligase 1	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 DNA ligase (ATP) activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion 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 DNA ligase (ATP) activity 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 DNA binding nucleic acid binding cation binding metal ion binding	DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process cell division cellular response to stimulus DNA-templated DNA replication lagging strand elongation primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA strand elongation DNA replication metabolic process cellular process DNA strand elongation involved in DNA replication macromolecule metabolic process cell division cellular response to stimulus mismatch repair response to stimulus cellular response to stress DNA damage response response to stress DNA repair mitotic DNA replication nuclear DNA replication cell cycle DNA replication Okazaki fragment processing involved in mitotic DNA replication mitotic cell cycle mitotic cell cycle process DNA replication, Okazaki fragment processing cell cycle cell cycle process developmental process anatomical structure morphogenesis anatomical structure development DNA recombination nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process DNA biosynthetic process base-excision repair base-excision repair, gap-filling	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
B	DNA chain 1	-	-	-
C	DNA chain 2	-	-	-
D	DNA chain 3	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036599	DNA ligase, ATP-dependent, N-terminal domain superfamily	Homologous Superfamily
A	IPR012310	DNA ligase, ATP-dependent, central	Domain
A	IPR012308	DNA ligase, ATP-dependent, N-terminal	Domain
A	IPR016059	DNA ligase, ATP-dependent, conserved site	Conserved Site
A	IPR000977	DNA ligase, ATP-dependent	Family
A	IPR050191	ATP-dependent DNA ligase	Family
A	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A	IPR012309	DNA ligase, ATP-dependent, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P18858	urinary bladder cancer adrenal cortex carcinoma medulloblastoma colorectal cancer osteosarcoma urinary bladder neoplasm malignant mesothelioma primitive neuroectodermal tumor xeroderma pigmentosum group G

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.