4U61 | pdb_00004u61

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with 6'-sialyllactose

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)
J	d4u61j_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
I	d4u61i_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
H	d4u61h_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
G	d4u61g_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
F	d4u61f_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
E	d4u61e_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
D	d4u61d_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
C	d4u61c_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
B	d4u61b_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)
A	d4u61a_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	Papovaviridae-like VP	automated matches	(Trichodysplasia spinulosa-associated polyomavirus ) [TaxId: 862909 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group I dsDNA viruses	8081599	3000939	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)
J	Polyoma_coat	e4u61J1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
I	Polyoma_coat	e4u61I1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
H	Polyoma_coat	e4u61H1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
G	Polyoma_coat	e4u61G1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
F	Polyoma_coat	e4u61F1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
E	Polyoma_coat	e4u61E1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
D	Polyoma_coat	e4u61D1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
C	Polyoma_coat	e4u61C1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
B	Polyoma_coat	e4u61B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)
A	Polyoma_coat	e4u61A1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Polyoma_coat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
I	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
H	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
G	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
F	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
E	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
D	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
C	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
B	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
A	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)

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	Structural protein VP1	structural molecule activity cation binding ion binding binding metal ion binding small molecule binding	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont 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 endocytosis involved in viral entry into host cell	viral capsid icosahedral viral capsid T=7 icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle

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	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR000662	Capsid protein VP1,Polyomavirus	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036931	Polyomavirus capsid protein VP1 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.