1Q3U | pdb_00001q3u

Crystal structure of a wild-type Cre recombinase-loxP synapse: pre-cleavage complex

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)
H [auth F]	d1q3uf1	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 F]	d1q3uf2	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 E]	d1q3ue1	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 E]	d1q3ue2	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)
F [auth B]	d1q3ub1	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)
F [auth B]	d1q3ub2	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)
E [auth A]	d1q3ua1	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)
E [auth A]	d1q3ua2	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)
H [auth F]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
H [auth F]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
G [auth E]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	lambda integrase clamp domain-like	8040147	3000550	SCOP2B (2022-06-29)
F [auth B]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
E [auth A]	SCOP2B Superfamily	DNA breaking-rejoining enzymes	8040148	3001127	SCOP2B (2022-06-29)
E [auth A]	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)
H [auth F]	Topoisom_I,Topo_C_assoc	e1q3uF1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Topoisom_I,Topo_C_assoc	ECOD (develop294)
H [auth F]	UBA	e1q3uF3	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (develop294)
G [auth E]	Topoisom_I,Topo_C_assoc	e1q3uE1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Topoisom_I,Topo_C_assoc	ECOD (develop294)
G [auth E]	UBA	e1q3uE3	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (develop294)
F [auth B]	Topoisom_I,Topo_C_assoc	e1q3uB1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Topoisom_I,Topo_C_assoc	ECOD (develop294)
F [auth B]	UBA	e1q3uB3	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (develop294)
E [auth A]	Topoisom_I,Topo_C_assoc	e1q3uA1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Topoisom_I,Topo_C_assoc	ECOD (develop294)
E [auth A]	UBA	e1q3uA3	A: alpha bundles	X: EGF-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: UBA	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth A], F [auth B], G [auth E], H [auth F]	IPR011010	DNA breaking-rejoining enzyme, catalytic core	Homologous Superfamily
E [auth A], F [auth B], G [auth E], H [auth F]	IPR010998	Integrase/recombinase, N-terminal	Homologous Superfamily
E [auth A], F [auth B], G [auth E], H [auth F]	IPR052925	Phage Integrase-like Recombinase	Family
E [auth A], F [auth B], G [auth E], H [auth F]	IPR044068	Core-binding (CB) domain	Domain
E [auth A], F [auth B], G [auth E], H [auth F]	IPR002104	Integrase, catalytic domain	Domain
E [auth A], F [auth B], G [auth E], H [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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.