6Y5X

Structure of apo New Jersey Polyomavirus VP1

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)
A	d6y5xa_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
B	d6y5xb_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
C	d6y5xc_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
D	d6y5xd_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
E	d6y5xe_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
F	d6y5xf_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
G	d6y5xg_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
H	d6y5xh_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
I	d6y5xi_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)
J	d6y5xj_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Group I dsDNA viruses	automated matches	automated matches	(New Jersey polyomavirus-2013 ) [TaxId: 1497391 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
G	SCOP2 Family	papovaviridae-like vp	8096007	4003485	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group I dsDNA viruses	8096008	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)
A	Polyoma_coat	e6y5xA1	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	e6y5xB1	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	e6y5xC1	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	e6y5xD1	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	e6y5xE1	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	e6y5xF1	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	e6y5xG1	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	e6y5xH1	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	e6y5xI1	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)
J	Polyoma_coat	e6y5xJ1	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)
A	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
B	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
C	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
D	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
E	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
F	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
G	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
H	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
I	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)
J	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)

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	VP1	structural molecule activity cation binding ion binding binding metal ion binding small molecule binding	-	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 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.