5GAI | pdb_00005gai

Probabilistic Structural Models of Mature P22 Bacteriophage Portal, Hub, and Tailspike proteins

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)
Z	SCOP2B Superfamily	Head-binding domain of phage P22 tailspike protein	8043159	3002008	SCOP2B (2022-06-29)
Z	SCOP2B Superfamily	Pectin lyase-like	8042982	3001746	SCOP2B (2022-06-29)
Y	SCOP2B Superfamily	Head-binding domain of phage P22 tailspike protein	8043159	3002008	SCOP2B (2022-06-29)
Y	SCOP2B Superfamily	Pectin lyase-like	8042982	3001746	SCOP2B (2022-06-29)
AA [auth 0]	SCOP2B Superfamily	Head-binding domain of phage P22 tailspike protein	8043159	3002008	SCOP2B (2022-06-29)
AA [auth 0]	SCOP2B Superfamily	Pectin lyase-like	8042982	3001746	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
R	SCOP2 Family	Phage P22 gp4-like	8046846	4005325	SCOP2 (2022-06-29)
R	SCOP2 Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2 (2022-06-29)
Q	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	YqbG/phage connector protein-like	8104062	3001980	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)
Z	Head_binding	e5gaiZ1	A: beta sandwiches	X: Head-binding domain of phage P22 tailspike protein (From Topology)	H: Head-binding domain of phage P22 tailspike protein (From Topology)	T: Head-binding domain of phage P22 tailspike protein	F: Head_binding	ECOD (1.6)
Z	PhageP22-tail_N	e5gaiZ3	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pectin lyase-like (From Topology)	T: Pectin lyase-like	F: PhageP22-tail_N	ECOD (1.6)
Z	PhageP22-tail_C	e5gaiZ2	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: PhageP22-tail_C	ECOD (1.6)
Y	Head_binding	e5gaiY2	A: beta sandwiches	X: Head-binding domain of phage P22 tailspike protein (From Topology)	H: Head-binding domain of phage P22 tailspike protein (From Topology)	T: Head-binding domain of phage P22 tailspike protein	F: Head_binding	ECOD (1.6)
Y	PhageP22-tail_N	e5gaiY3	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pectin lyase-like (From Topology)	T: Pectin lyase-like	F: PhageP22-tail_N	ECOD (1.6)
Y	PhageP22-tail_C	e5gaiY1	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: PhageP22-tail_C	ECOD (1.6)
AA [auth 0]	Head_binding	e5gai02	A: beta sandwiches	X: Head-binding domain of phage P22 tailspike protein (From Topology)	H: Head-binding domain of phage P22 tailspike protein (From Topology)	T: Head-binding domain of phage P22 tailspike protein	F: Head_binding	ECOD (1.6)
AA [auth 0]	PhageP22-tail_N	e5gai03	A: beta duplicates or obligate multimers	X: Single-stranded right-handed beta-helix	H: Pectin lyase-like (From Topology)	T: Pectin lyase-like	F: PhageP22-tail_N	ECOD (1.6)
AA [auth 0]	PhageP22-tail_C	e5gai01	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: PhageP22-tail_C	ECOD (1.6)
V	P22_Tail-4	e5gaiV1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
U	P22_Tail-4	e5gaiU1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
T	P22_Tail-4	e5gaiT1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
S	P22_Tail-4	e5gaiS1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
R	P22_Tail-4	e5gaiR1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
Q	P22_Tail-4	e5gaiQ1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
P	P22_Tail-4	e5gaiP1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
O	P22_Tail-4	e5gaiO1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
N	P22_Tail-4	e5gaiN1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
M	P22_Tail-4	e5gaiM1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
L	P22_Tail-4	e5gaiL1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
K	P22_Tail-4	e5gaiK1	A: alpha arrays	X: Hypothetical protein YqbG-like (From Topology)	H: Hypothetical protein YqbG-like (From Topology)	T: Hypothetical protein YqbG-like	F: P22_Tail-4	ECOD (1.6)
X	P22_portal_2nd	e5gaiX2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
X	P22_portal_1st	e5gaiX1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
W	P22_portal_2nd	e5gaiW2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
W	P22_portal_1st	e5gaiW1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
J	P22_portal_2nd	e5gaiJ2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
J	P22_portal_1st	e5gaiJ1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
I	P22_portal_2nd	e5gaiI2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
I	P22_portal_1st	e5gaiI1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
H	P22_portal_2nd	e5gaiH1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
H	P22_portal_1st	e5gaiH2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
G	P22_portal_2nd	e5gaiG2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
G	P22_portal_1st	e5gaiG1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
F	P22_portal_2nd	e5gaiF1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
F	P22_portal_1st	e5gaiF2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
E	P22_portal_2nd	e5gaiE2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
E	P22_portal_1st	e5gaiE1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
D	P22_portal_2nd	e5gaiD2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
D	P22_portal_1st	e5gaiD1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
C	P22_portal_2nd	e5gaiC1	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
C	P22_portal_1st	e5gaiC2	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
B	P22_portal_2nd	e5gaiB2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
B	P22_portal_1st	e5gaiB1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)
A	P22_portal_2nd	e5gaiA2	A: beta barrels	X: Barrel domain in upper collar protein (From Topology)	H: Barrel domain in upper collar protein (From Topology)	T: Barrel domain in upper collar protein	F: P22_portal_2nd	ECOD (1.6)
A	P22_portal_1st	e5gaiA1	A: alpha bundles	X: Alpha-helical domain in upper collar protein (From Topology)	H: Alpha-helical domain in upper collar protein (From Topology)	T: Alpha-helical domain in upper collar protein	F: P22_portal_1st	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth 0], Y, Z	PF09251	Salmonella phage P22 tail-spike (PhageP22-tail)	Salmonella phage P22 tail-spike	-	Repeat
AA [auth 0], Y, Z	PF09008	Head binding (Head_binding)	Head binding	The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively an ...	The head binding domain found in the Phage P22 tailspike protein contains two regular beta-sheets, A and B, oriented nearly perpendicular to each other and composed of five and three strands respectively. The topology of the strands is exclusively antiparallel. The tailspike protein trimerises through this domain, and the direction of the strands with respect to the molecular triad is almost parallel for beta-sheet A, whereas beta-sheet B is perpendicular to the triad, forming a dome-like structure. This domain is dispensable for thermostability and SDS resistance of the intact protein, and its deletion has only minor effects on tailspike folding kinetics [1].	Domain
K, L, M, N, O K, L, M, N, O, P, Q, R, S, T, U, V	PF11650	P22 tail accessory factor (P22_Tail-4)	P22 tail accessory factor	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, W, X	PF16510	Phage P22-like portal protein (P22_portal)	Phage P22-like portal protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth 0], Y, Z	Tail fiber protein	hydrolase activity, acting on glycosyl bonds endo-1,3-alpha-L-rhamnosidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity catalytic activity	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 virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell symbiont-mediated disruption of host anatomical structure symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure 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 virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell symbiont-mediated disruption of host anatomical structure 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 envelope symbiont entry into host cell disruption of anatomical structure in another organism symbiont entry into host cell via disruption of host cell envelope lipopolysaccharide symbiont-mediated disruption of host cell wall	virus tail, fiber virus tail virion component
K, L, M, N, O K, L, M, N, O, P, Q, R, S, T, U, V	Peptidoglycan hydrolase gp4	hydrolase activity catalytic activity	symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms viral life cycle symbiont-mediated disruption of host cell wall symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell via disruption of host cell wall peptidoglycan symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism symbiont genome ejection through host cell envelope symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms viral life cycle symbiont-mediated disruption of host cell wall symbiont-mediated disruption of host cell envelope symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell via disruption of host cell wall peptidoglycan symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism symbiont genome ejection through host cell envelope symbiont genome ejection through host cell envelope, short tail mechanism symbiont entry into host cell via disruption of host cell envelope	virus tail virion component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, W, X	Portal protein	-	virion assembly viral process viral life cycle viral genome packaging viral DNA genome packaging symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host symbiont genome ejection through host cell envelope, short tail mechanism biological process involved in interaction with host biological process involved in symbiotic interaction viral DNA genome packaging, headful	protein-containing complex viral capsid virion component viral portal complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth 0], Y, Z	IPR012332	Autotransporter, pectate lyase C-like domain superfamily	Homologous Superfamily
AA [auth 0], Y, Z	IPR015331	P22 tailspike C-terminal domain	Domain
AA [auth 0], Y, Z	IPR036730	Phage P22 tailspike-like, N-terminal domain superfamily	Homologous Superfamily
AA [auth 0], Y, Z	IPR009093	Bacteriophage P22 tailspike, N-terminal	Domain
AA [auth 0], Y, Z	IPR011050	Pectin lyase fold/virulence factor	Homologous Superfamily
K, L, M, N, O K, L, M, N, O, P, Q, R, S, T, U, V	IPR038258	Peptidoglycan hydrolase Gp4 superfamily	Homologous Superfamily
K, L, M, N, O K, L, M, N, O, P, Q, R, S, T, U, V	IPR020362	Tail accessory factor GP4	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, W, X	IPR032427	Phage P22-like portal protein	Family