1PDI | pdb_00001pdi

Fitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
R	d1pdir_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
Q	d1pdiq_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
P	d1pdip_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
O	d1pdio_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
N	d1pdin_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
M	d1pdim_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
L	d1pdil_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
K	d1pdik_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
J	d1pdij_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
I	d1pdii_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
H	d1pdih_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
G	d1pdig_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
F	d1pdif_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
E	d1pdie_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
D	d1pdid_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
C	d1pdic_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
B	d1pdib_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)
A	d1pdia_	Low resolution protein structures	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	Bacteriophage T4 3D cryo-EM reconstruction	(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)
R	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Receptor-binding domain of short tail fibre protein gp12	8033955	3001249	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Phage fibre proteins	8044403	3000351	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)
R	MMS1_N	e1pdiR1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
Q	MMS1_N	e1pdiQ1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
P	MMS1_N	e1pdiP1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
O	MMS1_N	e1pdiO1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
N	MMS1_N	e1pdiN1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
M	MMS1_N	e1pdiM1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
L	MMS1_N	e1pdiL1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
K	MMS1_N	e1pdiK1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
J	MMS1_N	e1pdiJ1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
I	MMS1_N	e1pdiI1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
H	MMS1_N	e1pdiH1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
G	MMS1_N	e1pdiG1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
F	MMS1_N	e1pdiF1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
E	MMS1_N	e1pdiE1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
D	MMS1_N	e1pdiD1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
C	MMS1_N	e1pdiC1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
B	MMS1_N	e1pdiB1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)
A	MMS1_N	e1pdiA1	A: alpha bundles	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF07484	Phage Tail Collar Domain (Collar)	Phage Tail Collar Domain	This region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in ...	This region is occasionally found in conjunction with Pfam:PF03335. Most of the family appear to be phage tail proteins; however some appear to be involved in other processes. For instance Swiss:Q03314 from Rhizobium leguminosarum may be involved in plant-microbe interactions ([1]). A related protein Swiss:Q9L3N1 is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (Swiss:P10930) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop ([2]) and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of Swiss:P10930 appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the 'collar'. The domain may bind SO4, however the residues accredited with this vary between the PDB file and the Swiss-Prot entry. The long unconserved region maybe due to domain swapping in and out of a loop or reflective of rapid evolution.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF09089	Phage short tail fibre protein gp12, middle domain (gp12-short_mid)	Phage short tail fibre protein gp12, middle domain	-	Repeat
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	PF14928	Short tail fibre protein receptor-binding domain (S_tail_recep_bd)	Short tail fibre protein receptor-binding domain	This domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	Short tail fiber protein	cation binding ion binding binding metal ion binding small molecule binding	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell entry receptor-mediated virion attachment to host cell viral process viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virus tail, fiber virus tail virion component virus tail, baseplate

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR037053	Phage tail collar domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR027448	Short tail fibre protein, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR044916	Short tail fibre protein, C-terminal superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR015173	Bacteriophage T4, Gp12	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R	IPR011083	Phage tail collar domain	Domain