1Z1B

Crystal structure of a lambda integrase dimer bound to a COC' core site

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F [auth A]	d1z1ba1	Alpha and beta proteins (a+b)	DNA-binding domain	DNA-binding domain	lambda integrase N-terminal domain	lambda integrase N-terminal domain	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
F [auth A]	d1z1ba2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Integrase (Int)	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
G [auth B]	d1z1bb1	Alpha and beta proteins (a+b)	DNA-binding domain	DNA-binding domain	lambda integrase N-terminal domain	lambda integrase N-terminal domain	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)
G [auth B]	d1z1bb2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Integrase (Int)	(Lambdavirus lambda ) [TaxId: 10710 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F [auth A]	SCOP2 Family	lambda integrase DNA-binding domain-like	8022701	4002502	SCOP2 (2022-06-29)
F [auth A]	SCOP2 Family	lambda integrase-like clamp domain-like	8091467	4001040	SCOP2 (2022-06-29)
F [auth A]	SCOP2 Superfamily	DNA-binding domain	8035081	3000183	SCOP2 (2022-06-29)
F [auth A]	SCOP2 Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2 (2022-06-29)
F [auth A]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	DNA-binding domain	8035081	3000183	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	lambda integrase clamp domain-like	8091468	3000550	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8036952	3001127	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)
F [auth A]	Phage_integrase_C	e1z1bA2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_C	ECOD (1.6)
F [auth A]	Phage_integrase_N_1	e1z1bA1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N_1	ECOD (1.6)
F [auth A]	Phage_int_SAM_3	e1z1bA3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_3	ECOD (1.6)
F [auth A]	Arm-DNA-bind_1	e1z1bA4	A: a+b two layers	X: DNA-binding domain	H: GCC-box binding domain-like (From Topology)	T: GCC-box binding domain-like	F: Arm-DNA-bind_1	ECOD (1.6)
G [auth B]	Phage_integrase_C	e1z1bB4	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_C	ECOD (1.6)
G [auth B]	Phage_integrase_N_1	e1z1bB2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N_1	ECOD (1.6)
G [auth B]	Phage_int_SAM_3	e1z1bB3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_3	ECOD (1.6)
G [auth B]	Arm-DNA-bind_1	e1z1bB1	A: a+b two layers	X: DNA-binding domain	H: GCC-box binding domain-like (From Topology)	T: GCC-box binding domain-like	F: Arm-DNA-bind_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F [auth A]	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)
F [auth A]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
F [auth A]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)
G [auth B]	3.30.160.60	Alpha Beta	2-Layer Sandwich	Double Stranded RNA Binding Domain	Classic Zinc Finger	CATH (4.3.0)
G [auth B]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G [auth B]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
F [auth A], G [auth B]	PF00589	Phage integrase family (Phage_integrase)	Phage integrase family	-	Family
F [auth A], G [auth B]	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
F [auth A], G [auth B]	PF02899	Phage integrase, N-terminal SAM-like domain (Phage_int_SAM_1)	Phage integrase, N-terminal SAM-like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C]	5'-D(CPTCPGPTPTPCPAPGPCPTPTPTPTPTPT)-3'	-	-	-
B [auth D]	5'-D(TPTPTPAPTPAPCPTPAPAPGPTPTPGPGPCPAPT)-3'	-	-	-
C [auth E]	29-MER DNA	-	-	-
D [auth F]	26-MER DNA	-	-	-
E [auth G]	26-MER DNA	-	-	-
F [auth A], G [auth B]	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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth A], G [auth B]	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
F [auth A], G [auth B]	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
F [auth A], G [auth B]	IPR015094	Integrase, lambda-type, N-terminal DNA-binding	Domain
F [auth A], G [auth B]	IPR044068	Core-binding (CB) domain	Domain
F [auth A], G [auth B]	IPR002104	Integrase, catalytic domain	Domain
F [auth A], G [auth B]	IPR004107	Integrase, SAM-like, N-terminal	Domain
F [auth A], G [auth B]	IPR013762	Integrase-like, catalytic domain superfamily	Homologous Superfamily
F [auth A], G [auth B]	IPR016177	DNA-binding domain superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F [auth A], G [auth B]	PTR	Parent Component: TYR RESID: AA0039 PSI-MOD : O4'-phospho-L-tyrosine MOD:00048

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.