3PKZ | pdb_00003pkz

Structural basis for catalytic activation of a serine recombinase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
L	d3pkzl_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
K	d3pkzk_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
J	d3pkzj_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
I	d3pkzi_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
H	d3pkzh_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
G	d3pkzg_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
F	d3pkzf_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
E	d3pkze_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
D	d3pkzd_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
C	d3pkzc_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
B	d3pkzb_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)
A	d3pkza_	Alpha and beta proteins (a/b)	Resolvase-like	Resolvase-like	automated matches	automated matches	(Staphylococcus aureus ) [TaxId: 1280 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Resolvase-like	8071362	3000065	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Resolvase-like	8071362	3000065	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)
L	YjeF_N	e3pkzL1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
K	YjeF_N	e3pkzK1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
J	YjeF_N	e3pkzJ1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
I	YjeF_N	e3pkzI1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
H	YjeF_N	e3pkzH1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
G	YjeF_N	e3pkzG1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
F	YjeF_N	e3pkzF1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
E	YjeF_N	e3pkzE1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
D	YjeF_N	e3pkzD1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
C	YjeF_N	e3pkzC1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
B	YjeF_N	e3pkzB1	A: a/b three-layered sandwiches	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: YjeF_N	ECOD (v294.1)
A	Cytochrom_C	e3pkzA1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: Cytochrom_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
K	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
J	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
I	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
H	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
G	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
F	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
E	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
D	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
C	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
B	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)
A	3.40.50.1390	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Resolvase, N-terminal catalytic domain	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	Recombinase Sin	DNA binding binding nucleic acid binding catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA strand exchange activity catalytic activity	nucleobase-containing compound metabolic process metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process transposition	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR036162	Resolvase-like, N-terminal catalytic domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006118	Recombinase, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006119	Resolvase, N-terminal catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006120	Resolvase, HTH domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR050639	Site-specific recombinase resolvase	Family

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.