4QKO | pdb_00004qko

The Crystal Structure of the Pyocin S2 Nuclease Domain, Immunity Protein Complex at 1.8 Angstroms

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)
D	d4qkod_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
F	d4qkof_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
H	d4qkoh_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
B	d4qkob_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
A	d4qkoa_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
C	d4qkoc_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
E	d4qkoe_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)
G	d4qkog_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	automated matches	automated matches	(Pseudomonas aeruginosa PAO1 ) [TaxId: 208964 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	HNH-motif	8074113	4000889	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	His-Me finger endonucleases	8074114	3001893	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	His-Me finger endonucleases	8074114	3001893	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	His-Me finger endonucleases	8074114	3001893	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	His-Me finger endonucleases	8074114	3001893	SCOP2B (2022-06-29)
A	SCOP2 Family	Colicin E immunity proteins	8074109	4000862	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Colicin E immunity proteins	8074110	3001814	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Colicin E immunity proteins	8074110	3001814	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Colicin E immunity proteins	8074110	3001814	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Colicin E immunity proteins	8074110	3001814	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)
D	OB_Dis3	e4qkoD1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
F	OB_Dis3	e4qkoF1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
H	OB_Dis3	e4qkoH1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
B	OB_Dis3	e4qkoB1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
A	OB_Dis3	e4qkoA1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
C	OB_Dis3	e4qkoC1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
E	OB_Dis3	e4qkoE1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)
G	OB_Dis3	e4qkoG1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: OB_Dis3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
F	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
H	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
B	3.90.540.10	Alpha Beta	Alpha-Beta Complex	Colicin E7 immunity protein	Chain B, fragment: Endonuclease domain	CATH (4.3.0)
A	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
C	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
E	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)
G	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF21431	Colicin/Pyocin-S2, DNase domain (Col-Pyo_DNase)	Colicin/Pyocin-S2, DNase domain	This entry represents the DNAse domain from colicin/pyocin bacteriocins, such as pyocin-S2 from Pseudomonas aeruginosa and colicin E7/E9 from E. coli. This domain has an alpha/beta fold containing a Zn2+ ion binding site [1-5].	Domain
A, C, E, G	PF01320	Colicin immunity protein / pyocin immunity protein (Colicin_Pyocin)	Colicin immunity protein / pyocin immunity protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F, H	Pyocin-S2	protein binding binding signaling receptor binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid cation binding ion binding metal ion binding small molecule binding	cellular process cytolysis biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus cellular process cytolysis biological process involved in interspecies interaction between organisms disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus	-
A, C, E, G	Pyocin-S2 immunity protein	binding toxic substance binding	metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR016128	Pyosin/cloacin translocation domain	Domain
B, D, F, H	IPR044925	His-Me finger superfamily	Homologous Superfamily
B, D, F, H	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
B, D, F, H	IPR037146	Colicin/pyocin, DNase domain superfamily	Homologous Superfamily
B, D, F, H	IPR003060	Pyocin S killer protein	Family
B, D, F, H	IPR003615	HNH nuclease	Domain
A, C, E, G	IPR000290	Colicin immunity protein/pyocin immunity protein	Family
A, C, E, G	IPR035900	Colicin E immunity protein 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.