6Y5Y | pdb_00006y5y

Structure of New Jersey Polyomavirus VP1 in complex with 3'-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)
A	d6y5ya_	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	d6y5yb_	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	d6y5ye_	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	d6y5yf_	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	d6y5yj_	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	d6y5yi_	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	d6y5yh_	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	d6y5yg_	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	d6y5yd_	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	d6y5yc_	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)
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)
J	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)
H	SCOP2B Superfamily	Group I dsDNA viruses	8096008	3000939	SCOP2B (2022-06-29)
G	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)
C	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	Pro_isomerase	e6y5yA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
B	Urm1	e6y5yB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Urm1	ECOD (v294.1)
E	Pro_isomerase	e6y5yE1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
F	Pro_isomerase	e6y5yF1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
J	Pro_isomerase	e6y5yJ1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
I	Pro_isomerase	e6y5yI1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
H	Pro_isomerase	e6y5yH1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
G	Pro_isomerase	e6y5yG1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
D	Pro_isomerase	e6y5yD1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)
C	Pro_isomerase	e6y5yC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Pro_isomerase	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	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	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.