2GYK | pdb_00002gyk

Crystal structure of the complex of the Colicin E9 DNase domain with a mutant immunity protein, IMME9 (D51A)

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)
D [auth F]	d2gykf_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH-motif	DNase domain of colicin E9	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2gykb_	Alpha and beta proteins (a+b)	His-Me finger endonucleases	His-Me finger endonucleases	HNH-motif	DNase domain of colicin E9	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth E]	d2gyke_	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	Colicin E immunity proteins	ImmE9 protein (Im9)	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2gyka1	All alpha proteins	Acyl carrier protein-like	Colicin E immunity proteins	Colicin E immunity proteins	ImmE9 protein (Im9)	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth F]	SCOP2B Superfamily	His-Me finger endonucleases	8042111	3001893	SCOP2B (2022-06-29)
B	SCOP2 Family	HNH-motif	8029732	4000889	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	His-Me finger endonucleases	8042111	3001893	SCOP2 (2022-06-29)
C [auth E]	SCOP2B Superfamily	Colicin E immunity proteins	8037581	3001814	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Colicin E immunity proteins	8037581	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 [auth F]	zf-His_Me_endon	e2gykF1	A: a/b three-layered sandwiches	X: EGF-like	H: EGF-related	T: EGF/Laminin	F: zf-His_Me_endon	ECOD (v294.1)
B	Col-Pyo_DNase	e2gykB1	A: few secondary structure elements	X: His-Me finger endonucleases	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: Col-Pyo_DNase	ECOD (v294.1)
C [auth E]		e2gykE1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)
A		e2gykA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Flavivirus capsid protein C	T: Flavivirus capsid protein C	F:	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth F]	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)
C [auth E]	1.10.1200.20	Mainly Alpha	Orthogonal Bundle	Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein	Chain A	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth F]	Colicin-E9	protein binding binding protein domain specific 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	biological process involved in interspecies interaction between organisms cellular process 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 biological process involved in interspecies interaction between organisms cellular process 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	intracellular anatomical structure cellular anatomical structure extrachromosomal circular DNA extrachromosomal DNA protein-containing complex
A, C [auth E]	Colicin-E9 immunity protein	protein binding binding protein domain specific binding toxic substance binding	metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D [auth F]	IPR024575	Cloacin/colicin	Family
B, D [auth F]	IPR016128	Pyosin/cloacin translocation domain	Domain
B, D [auth F]	IPR044925	His-Me finger superfamily	Homologous Superfamily
B, D [auth F]	IPR024566	Colicin, receptor domain	Domain
B, D [auth F]	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
B, D [auth F]	IPR037146	Colicin/pyocin, DNase domain superfamily	Homologous Superfamily
A, C [auth E]	IPR000290	Colicin immunity protein/pyocin immunity protein	Family
A, C [auth E]	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.