3EZK | pdb_00003ezk

Bacteriophage T4 gp17 motor assembly based on crystal structures and cryo-EM reconstructions

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribonuclease H-like	8092505	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8092504	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RecA-like P-loop NTPases	8092504	3002019	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease H-like	8092505	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribonuclease H-like	8092505	3000143	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RecA-like P-loop NTPases	8092504	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8092504	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8092505	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribonuclease H-like	8092505	3000143	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RecA-like P-loop NTPases	8092504	3002019	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)
A	Terminase_6	e3ezkA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6	ECOD (1.6)
A	Terminase_6C	e3ezkA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Terminase_6C	ECOD (1.6)
C	Terminase_6	e3ezkC1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6	ECOD (1.6)
C	Terminase_6C	e3ezkC2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Terminase_6C	ECOD (1.6)
D	Terminase_6	e3ezkD1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6	ECOD (1.6)
D	Terminase_6C	e3ezkD2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Terminase_6C	ECOD (1.6)
B	Terminase_6	e3ezkB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6	ECOD (1.6)
B	Terminase_6C	e3ezkB2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Terminase_6C	ECOD (1.6)
E	Terminase_6	e3ezkE1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Terminase_6	ECOD (1.6)
E	Terminase_6C	e3ezkE2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Terminase_6C	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF17289	Terminase RNaseH-like domain (Terminase_6C)	Terminase RNaseH-like domain		Domain
A, B, C, D, E	PF03237	Terminase large subunit, T4likevirus-type, N-terminal (Terminase_6N)	Terminase large subunit, T4likevirus-type, N-terminal	This entry represents the N-terminal domain of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. It includes the terminase large subunit of Bacteriophage T4 (terminase gene 17, Gp17) [1,3]. Hom ...	This entry represents the N-terminal domain of terminase large subunits found in a variety of the Caudovirales and prophage regions of bacterial genomes. It includes the terminase large subunit of Bacteriophage T4 (terminase gene 17, Gp17) [1,3]. Homologues are also found in Gene Transfer Agents (GTA) [2], including ORFg2 (RCAP_rcc01683) of the GTA of Rhodobacter capsulatus (Rhodopseudomonas capsulata) [see Fig.1, in 4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	DNA packaging protein Gp17	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides ATP-dependent activity endonuclease activity cation binding metal ion binding	virus maturation viral life cycle viral capsid assembly viral procapsid maturation cellular component biogenesis cellular component organization virion assembly cellular component assembly viral process cellular process cellular component organization or biogenesis organelle organization chromosome organization viral genome packaging virus maturation viral life cycle viral capsid assembly viral procapsid maturation cellular component biogenesis cellular component organization virion assembly cellular component assembly viral process cellular process cellular component organization or biogenesis organelle organization chromosome organization viral genome packaging viral DNA genome packaging	viral terminase complex protein-containing complex catalytic complex viral terminase, large subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR044267	Terminase, large subunit, gp17-like	Family
A, B, C, D, E	IPR035421	Terminase, large subunit gp17-like, C-terminal	Domain
A, B, C, D, E	IPR027417	P-loop containing nucleoside triphosphate hydrolase	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.