6HKU | pdb_00006hku

Trichodysplasia spinulosa-associated polyomavirus (TSPyV) VP1 in complex with sialylated precision glycooligomers

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
J	d6hkuj_	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	d6hkui_	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	d6hkuh_	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	d6hkug_	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	d6hkuf_	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	d6hkue_	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	d6hkud_	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	d6hkuc_	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	d6hkub_	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	d6hkua_	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	LptF_LptG	e6hkuJ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
I	LptF_LptG	e6hkuI1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
H	LptF_LptG	e6hkuH1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
G	LptF_LptG	e6hkuG1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
F	LptF_LptG	e6hkuF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
E	LptF_LptG	e6hkuE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
D	LptF_LptG	e6hkuD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
C	LptF_LptG	e6hkuC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
B	LptF_LptG	e6hkuB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: LptF_LptG	ECOD (v294.1)
A	RsmJ	e6hkuA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: RsmJ	ECOD (v294.1)

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 (utative)
I	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)
G	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)
E	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)
C	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)
A	2.60.175.10	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (utative)

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	PF00718	Polyomavirus coat protein (Polyoma_coat)	Polyomavirus coat protein		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	Capsid 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.