Annotations: 5J0N

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA-binding domain	8035081	3000183	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA-binding domain	8035081	3000183	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA-binding domain	8035081	3000183	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034409	3000426	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034409	3000426	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034410	3000426	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	IHF-like DNA-binding proteins	8034410	3000426	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Putative DNA-binding domain	8038870	3000158	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)
E	PF00589	e5j0nE3	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: PF00589	ECOD (1.6)
E	PF02899	e5j0nE1	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: PF02899	ECOD (1.6)
F	PF00589	e5j0nF4	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: PF00589	ECOD (1.6)
F	PF02899	e5j0nF1	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: PF02899	ECOD (1.6)
F	PF09003	e5j0nF2	A: a+b two layers	X: DNA-binding domain	H: GCC-box binding domain-like (From Topology)	T: GCC-box binding domain-like	F: PF09003	ECOD (1.6)
G	PF00589	e5j0nG4	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: PF00589	ECOD (1.6)
G	PF02899	e5j0nG2	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: PF02899	ECOD (1.6)
G	PF09003	e5j0nG1	A: a+b two layers	X: DNA-binding domain	H: GCC-box binding domain-like (From Topology)	T: GCC-box binding domain-like	F: PF09003	ECOD (1.6)
H	PF00589	e5j0nH4	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: PF00589	ECOD (1.6)
H	PF02899	e5j0nH3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: PF02899	ECOD (1.6)
H	PF09003	e5j0nH1	A: a+b two layers	X: DNA-binding domain	H: GCC-box binding domain-like (From Topology)	T: GCC-box binding domain-like	F: PF09003	ECOD (1.6)
I	PF00216	e5j0nI1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
K	PF00216	e5j0nK1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
J	PF00216	e5j0nJ1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
L	PF00216	e5j0nL1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
M	PF07825	e5j0nM1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PF07825	ECOD (1.6)
N	PF07825	e5j0nN1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PF07825	ECOD (1.6)
O	PF07825	e5j0nO1	A: alpha arrays	X: HTH	H: HTH	T: Putative DNA-binding domain	F: PF07825	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E, F, G, H	PF00589	Phage integrase family (Phage_integrase)	Phage integrase family	-	Family
E, F, G, H	PF09003	Bacteriophage lambda integrase, Arm DNA-binding domain (Arm-DNA-bind_1)	Bacteriophage lambda integrase, Arm DNA-binding domain	The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA- ...	The amino terminal domain of bacteriophage lambda integrase folds into a three-stranded, antiparallel beta-sheet that packs against a C-terminal alpha-helix, adopting a fold that is structurally related to the three-stranded beta-sheet family of DNA-binding domains (which includes the GCC-box DNA-binding domain and the N-terminal domain of Tn916 integrase). This domain is responsible for high-affinity binding to each of the five DNA arm-type sites and is also a context-sensitive modulator of DNA cleavage [1].	Domain
E, F, G, H	PF02899	Phage integrase, N-terminal SAM-like domain (Phage_int_SAM_1)	Phage integrase, N-terminal SAM-like domain	-	Domain
I, K	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein	-	Domain
J, L	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein	-	Domain
M, N, O	PF07825	Excisionase-like protein (Exc)	Excisionase-like protein	The phage-encoded excisionase protein (Xis, Swiss:P03699) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha ...	The phage-encoded excisionase protein (Xis, Swiss:P03699) is involved in excisive recombination by regulating the assembly of the excisive intasome and by inhibiting viral integration. It adopts an unusual 'winged'-helix structure in which two alpha helices are packed against two extended strands. Also present in the structure is a two-stranded anti-parallel beta-sheet, whose strands are connected by a four-residue 'wing'. During interaction with DNA, helix alpha2 is thought to insert into the major groove, while the wing contacts the adjacent minor groove or phosphodiester backbone. The C-terminal region of Xis is involved in interaction with phage-encoded integrase (Int), and a putative C-terminal alpha helix may fold upon interaction with Int and/or DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	attP(-117 to +79)	-	-	-
B	attB(-21) to attP(+117)	-	-	-
C	attB(-19 to +21)	-	-	-
D	attP(-79) to attB(+19)	-	-	-
E, F, G, H	Integrase	DNA binding binding organic cyclic compound binding nucleic acid binding hydrolase activity catalytic activity transferase activity integrase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid	establishment of integrated proviral latency viral latency viral process establishment of viral latency biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process establishment of integrated proviral latency viral latency viral process establishment of viral latency biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process viral genome integration into host DNA DNA recombination provirus excision latent virus replication release from viral latency	-
I, K	Integration host factor subunit alpha	DNA binding binding organic cyclic compound binding nucleic acid binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity structural molecule activity structural constituent of chromatin	regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process organic cyclic compound biosynthetic process DNA recombination DNA metabolic process	bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex IHF-DNA complex nucleoid cellular anatomical entity DNA bending complex intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle cytoplasm cytosol
J, L	Integration host factor subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of chromatin	regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process cellular process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process organonitrogen compound biosynthetic process post-transcriptional regulation of gene expression protein metabolic process organonitrogen compound metabolic process regulation of protein metabolic process translation regulation of translation DNA recombination DNA metabolic process	bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex IHF-DNA complex nucleoid cellular anatomical entity DNA bending complex intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome cytoplasm bacterial nucleoid protein-containing complex intracellular anatomical structure protein-DNA complex IHF-DNA complex nucleoid cellular anatomical entity DNA bending complex intracellular organelle organelle intracellular non-membrane-bounded organelle non-membrane-bounded organelle chromosome cytoplasm cytosol
M, N, O	Excisionase	DNA binding binding organic cyclic compound binding nucleic acid binding identical protein binding protein binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process DNA recombination metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process provirus excision latent virus replication viral latency viral process release from viral latency	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E, F, G, H	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
E, F, G, H	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
E, F, G, H	IPR015094	Integrase, lambda-type, N-terminal DNA-binding	Domain
E, F, G, H	IPR044068	Core-binding (CB) domain	Domain
E, F, G, H	IPR002104	Integrase, catalytic domain	Domain
E, F, G, H	IPR004107	Integrase, SAM-like, N-terminal	Domain
E, F, G, H	IPR013762	Integrase-like, catalytic domain superfamily	Homologous Superfamily
E, F, G, H	IPR016177	DNA-binding domain superfamily	Homologous Superfamily
I, K	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
I, K	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
I, K	IPR005684	Integration host factor, alpha subunit	Family
I, K	IPR000119	Histone-like DNA-binding protein	Family
J, L	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
J, L	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
J, L	IPR005685	Integration host factor, beta subunit	Family
J, L	IPR000119	Histone-like DNA-binding protein	Family
M, N, O	IPR012884	Excisionase-like	Domain
M, N, O	IPR038137	Excisionase-like superfamily	Homologous Superfamily
M, N, O	IPR009061	Putative DNA-binding domain superfamily	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.