1Q3V

Crystal structure of a wild-type Cre recombinase-loxP synapse: phosphotyrosine covalent intermediate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I [auth E]	d1q3ve1	All alpha proteins	SAM domain-like	lambda integrase-like, N-terminal domain	lambda integrase-like, N-terminal domain	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
I [auth E]	d1q3ve2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
G [auth A]	d1q3va1	All alpha proteins	SAM domain-like	lambda integrase-like, N-terminal domain	lambda integrase-like, N-terminal domain	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
G [auth A]	d1q3va2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
H [auth B]	d1q3vb1	All alpha proteins	SAM domain-like	lambda integrase-like, N-terminal domain	lambda integrase-like, N-terminal domain	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
H [auth B]	d1q3vb2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
J [auth F]	d1q3vf1	All alpha proteins	SAM domain-like	lambda integrase-like, N-terminal domain	lambda integrase-like, N-terminal domain	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)
J [auth F]	d1q3vf2	Alpha and beta proteins (a+b)	DNA breaking-rejoining enzymes	DNA breaking-rejoining enzymes	Lambda integrase-like, catalytic core	Cre recombinase	(Punavirus P1 ) [TaxId: 10678 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth E]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
I [auth E]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
J [auth F]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	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)
I [auth E]	INT_Cre_C	e1q3vE2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: INT_Cre_C	ECOD (1.6)
I [auth E]	Phage_integrase_N	e1q3vE1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
I [auth E]	Phage_int_SAM_4	e1q3vE3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_4	ECOD (1.6)
G [auth A]	INT_Cre_C	e1q3vA2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: INT_Cre_C	ECOD (1.6)
G [auth A]	Phage_integrase_N	e1q3vA1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
G [auth A]	Phage_int_SAM_4	e1q3vA3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_4	ECOD (1.6)
H [auth B]	INT_Cre_C	e1q3vB2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: INT_Cre_C	ECOD (1.6)
H [auth B]	Phage_integrase_N	e1q3vB1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
H [auth B]	Phage_int_SAM_4	e1q3vB3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_4	ECOD (1.6)
J [auth F]	INT_Cre_C	e1q3vF2	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: INT_Cre_C	ECOD (1.6)
J [auth F]	Phage_integrase_N	e1q3vF1	A: alpha arrays	X: HTH	H: HTH	T: DNA breaking-rejoining enzymes	F: Phage_integrase_N	ECOD (1.6)
J [auth F]	Phage_int_SAM_4	e1q3vF3	A: alpha arrays	X: lambda integrase-N-like	H: lambda integrase-N (From Topology)	T: lambda integrase-N	F: Phage_int_SAM_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I [auth E]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)
I [auth E]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G [auth A]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)
G [auth A]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
H [auth B]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)
H [auth B]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
J [auth F]	1.10.443.10	Mainly Alpha	Orthogonal Bundle	hpI Integrase	Chain A	CATH (4.3.0)
J [auth F]	1.10.150.130	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B], I [auth E], J [auth F]	PF00589	Phage integrase family (Phage_integrase)	Phage integrase family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], D [auth G]	loxP DNA	-	-	-
B [auth X], E [auth Y]	loxP DNA	-	-	-
C [auth D], F [auth H]	loxP DNA	-	-	-
G [auth A], H [auth B], I [auth E], J [auth F]	Cre recombinase	DNA binding binding nucleic acid binding	nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process DNA recombination	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B], I [auth E], J [auth F]	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
G [auth A], H [auth B], I [auth E], J [auth F]	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
G [auth A], H [auth B], I [auth E], J [auth F]	IPR052925	Phage Integrase-like Recombinase	Family
G [auth A], H [auth B], I [auth E], J [auth F]	IPR044068	Core-binding (CB) domain	Domain
G [auth A], H [auth B], I [auth E], J [auth F]	IPR002104	Integrase, catalytic domain	Domain
G [auth A], H [auth B], I [auth E], J [auth F]	IPR013762	Integrase-like, catalytic 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 R01GM157729.