1K28

The Structure of the Bacteriophage T4 Cell-Puncturing Device

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)
B [auth D]	d1k28d1	All beta proteins	Phage tail proteins	Phage tail proteins	Baseplate protein-like	Baseplate structural protein gp27	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1k28a1	All beta proteins	OB-fold	gp5 N-terminal domain-like	gp4 N-terminal domain-like	Tail-associated lysozyme gp5, N-terminal domain	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1k28a2	All beta proteins	Triple-stranded beta-helix	Phage fibre proteins	Tail-associated lysozyme gp5, C-terminal domain	Tail-associated lysozyme gp5, C-terminal domain	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1k28a3	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	Phage lysozyme	Tail-associated lysozyme gp5, catalytic domain	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1k28a4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth D]	SCOP2 Family	Baseplate protein-like	8025372	4003106	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Family	Baseplate protein-like	8025374	4003106	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Phage tail proteins	8037751	3000268	SCOP2 (2022-06-29)
B [auth D]	SCOP2 Superfamily	Phage tail proteins	8037753	3000268	SCOP2 (2022-06-29)
A	SCOP2 Family	gp4 N-terminal domain-like	8025366	4003074	SCOP2 (2022-06-29)
A	SCOP2 Family	Tail-associated lysozyme gp5, C-terminal domain	8025367	4003154	SCOP2 (2022-06-29)
A	SCOP2 Family	Phage lysozyme	8025370	4000895	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	gp5 N-terminal domain-like	8037745	3000235	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Phage fibre proteins	8037746	3000351	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Lysozyme-like	8037749	3001879	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth D]	Phage-tail_1_N	e1k28D5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage-tail_1_N	ECOD (1.6)
B [auth D]	Phage-tail_2_2nd	e1k28D2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage-tail_2_2nd	ECOD (1.6)
B [auth D]	Phage-tail_1_C	e1k28D6	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: Phage-tail_1_C	ECOD (1.6)
B [auth D]	Phage-tail_2_1st	e1k28D4	A: a+b complex topology	X: C-terminal insertion domain in phage tail proteins (From Topology)	H: C-terminal insertion domain in phage tail proteins (From Topology)	T: C-terminal insertion domain in phage tail proteins	F: Phage-tail_2_1st	ECOD (1.6)
A	Gp5_OB	e1k28A1	A: beta barrels	X: OB-fold	H: Tail-associated lysozyme gp5-N (From Topology)	T: Tail-associated lysozyme gp5-N	F: Gp5_OB	ECOD (1.6)
A	5	e1k28A2	A: beta duplicates or obligate multimers	X: Phage tail fiber protein trimerization domain (From Topology)	H: Phage tail fiber protein trimerization domain (From Topology)	T: Phage tail fiber protein trimerization domain	F: 5	ECOD (1.6)
A	Phage_lysozyme_2	e1k28A3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Phage_lysozyme_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth D]	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
B [auth D]	3.55.50.20	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold		CATH (4.3.0)
B [auth D]	2.40.30.150	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B [auth D]	3.30.1920.40	Alpha Beta	2-Layer Sandwich	Phage tail proteins - 2 layer sandwich fold		CATH (4.3.0)
A	2.40.50.260	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding protein domain	CATH (4.3.0)
A	3.10.450.190	Alpha Beta	Roll	Nuclear Transport Factor 2	Chain: A,	CATH (4.3.0)
A	1.10.530.40	Mainly Alpha	Orthogonal Bundle	Lysozyme		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth D]	PF09096	Baseplate structural protein, domain 2 (Phage-tail_2)	Baseplate structural protein, domain 2	Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27 [ ...	Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27 [1].	Domain
B [auth D]	PF09097	Baseplate structural protein, domain 1 (Phage-tail_1)	Baseplate structural protein, domain 1	Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27 [ ...	Members of this family adopt a beta barrel structure with a Greek key topology, which is topologically similar to the FMN-binding split barrel. They are structural component of the viral baseplate, predominantly found in the structural protein gp27 [1].	Domain
A	PF00959	Phage lysozyme (Phage_lysozyme)	Phage lysozyme	This family includes lambda phage lysozyme and E. coli endolysin.	Domain
A	PF06715	Gp5 C-terminal repeat (3 copies) (Gp5_C)	Gp5 C-terminal repeat (3 copies)	-	Repeat
A	PF06714	Gp5 N-terminal OB domain (Gp5_OB)	Gp5 N-terminal OB domain	This domain is found at the N terminus of the Gp5 baseplate protein of bacteriophage T4. This domain binds to the Gp27 protein [1]. This domain has the common OB fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D]	BASEPLATE STRUCTURAL PROTEIN GP27	-	virion assembly viral tail assembly viral process viral life cycle	virus tail virion component virus tail, baseplate
A	TAIL-ASSOCIATED LYSOZYME	hydrolase activity, acting on glycosyl bonds peptidoglycan muralytic activity hydrolase activity, hydrolyzing O-glycosyl compounds lysozyme activity hydrolase activity catalytic activity identical protein binding protein binding binding	biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated disruption of host anatomical structure viral life cycle disruption of cell wall in another organism symbiont-mediated disruption of host cell wall symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell wall peptidoglycan disruption of cellular anatomical structure in another organism symbiont entry into host cell viral process biological process involved in interspecies interaction between organisms symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated disruption of host anatomical structure viral life cycle disruption of cell wall in another organism symbiont-mediated disruption of host cell wall symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure symbiont entry into host cell via disruption of host cell wall peptidoglycan disruption of cellular anatomical structure in another organism symbiont entry into host cell viral process disruption of anatomical structure in another organism symbiont entry into host cell via disruption of host cell envelope virion assembly viral tail assembly catabolic process cell wall organization or biogenesis metabolic process cellular process macromolecule metabolic process macromolecule catabolic process cell wall macromolecule catabolic process cell wall macromolecule metabolic process disruption of cell in another organism killing of cells of another organism cell killing response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus carbohydrate derivative catabolic process peptidoglycan catabolic process glycosaminoglycan metabolic process carbohydrate derivative metabolic process aminoglycan catabolic process glycosaminoglycan catabolic process aminoglycan metabolic process peptidoglycan metabolic process	virus tail virion component virus tail, baseplate

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D]	IPR015180	Bacteriophage T4, Gp27, baseplate hub, C-terminal	Domain
B [auth D]	IPR043084	Gp27, baseplate hub, domain 4	Homologous Superfamily
B [auth D]	IPR043083	Gp27, baseplate hub, domain 3	Homologous Superfamily
B [auth D]	IPR043085	Gp27, baseplate hub, domain 2	Homologous Superfamily
B [auth D]	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold	Homologous Superfamily
B [auth D]	IPR015181	Bacteriophage T4, Gp27, baseplate hub, N-terminal	Domain
A	IPR052619	Bacteriophage lysozyme-like	Family
A	IPR009590	Protein Gp5, N-terminal OB-fold domain	Domain
A	IPR023347	Lysozyme domain superfamily	Homologous Superfamily
A	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily
A	IPR046397	Pre-baseplate central spike protein Gp5	Family
A	IPR001165	T4-type lysozyme	Family
A	IPR010609	Gp5, C-terminal	Repeat
A	IPR002196	Glycoside hydrolase, family 24	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.