1X9N | pdb_00001x9n

Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D [auth A]	d1x9na1	All alpha proteins	ATP-dependent DNA ligase DNA-binding domain	ATP-dependent DNA ligase DNA-binding domain	ATP-dependent DNA ligase DNA-binding domain	DNA ligase I (LIG1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d1x9na2	All beta proteins	OB-fold	Nucleic acid-binding proteins	DNA ligase/mRNA capping enzyme postcatalytic domain	DNA ligase I (LIG1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d1x9na3	Alpha and beta proteins (a+b)	ATP-grasp	DNA ligase/mRNA capping enzyme, catalytic domain	ATP-dependent DNA ligase catalytic domain	DNA ligase I (LIG1)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2 Family	ATP-dependent DNA ligase DNA-binding domain	8031340	4002991	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Family	DNA ligase/mRNA capping enzyme postcatalytic domain-like	8031342	4001931	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Family	ATP-dependent DNA ligase catalytic domain	8031344	4002079	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	ATP-dependent DNA ligase DNA-binding domain	8043718	3001985	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	Nucleic acid-binding proteins	8043720	3000135	SCOP2 (2022-06-29)
D [auth A]	SCOP2 Superfamily	DNA ligase/mRNA capping enzyme, catalytic domain	8043722	3000798	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth A]		e1x9nA1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleic acid-binding protein	T: DNA_ligase_A_C	F:	ECOD (20:10:01)
D [auth A]		e1x9nA2	A: ATP-dependent DNA ligase DNA-binding domain	X: ATP-dependent DNA ligase DNA-binding domain	H: ATP-dependent DNA ligase DNA-binding domain	T: DNA_ligase_A_N	F:	ECOD (20:10:01)
D [auth A]		e1x9nA4	A: Protein kinase/SAICAR synthase/ATP-grasp	X: Protein kinase/SAICAR synthase/ATP-grasp	H: ATP-grasp	T: DNA_ligase_A_M	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth 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)
D [auth A]	3.30.1490.70	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D [auth A]	3.30.470.30	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
D [auth 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
D [auth A]	PF04675	DNA ligase N terminus (DNA_ligase_A_N)	DNA ligase N terminus	-	Family
D [auth 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
D [auth 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 [auth B]	dideoxy terminated DNA	-	-	-
B [auth C]	5'-phosphorylated DNA	-	-	-
C [auth D]	template DNA	-	-	-
D [auth A]	DNA ligase I	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 telomere organization chromosome organization telomere maintenance via semi-conservative replication telomere maintenance cellular component organization organelle organization cellular component organization or biogenesis base-excision repair base-excision repair, gap-filling	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.