6PPB | pdb_00006ppb

Kaposi's sarcoma-associated herpesvirus (KSHV), C5 portal vertex structure

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
S [auth 3]	EBV-NA1	e6ppb31	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: EBV-NA1	ECOD (v294.1)
R [auth 2]	EBV-NA1	e6ppb21	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: EBV-NA1	ECOD (v294.1)
Q [auth 1]	EBV-NA1	e6ppb11	A: a/b three-layered sandwiches	X: P-loop domains-like	H: DUF1107-like	T: DUF1107-like	F: EBV-NA1	ECOD (v294.1)
P [auth 0]	MAM33	e6ppb01	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: MAM33	ECOD (v294.1)
B [auth l]		e6ppbl01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F:	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
K [auth c], L [auth d], N [auth 6], O [auth 7]	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family
J [auth b], M [auth 5]	PF03327	Herpesvirus capsid shell protein VP19C (Herpes_VP19C)	Herpesvirus capsid shell protein VP19C	-	Family
F [auth S], G [auth T], H [auth W], I [auth X]	PF03122	Herpes virus major capsid protein (Herpes_MCP)	Herpes virus major capsid protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
P [auth 0], Q [auth 1], R [auth 2], S [auth 3]	Small capsomere-interacting protein	-	viral process	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
K [auth c], L [auth d], N [auth 6], O [auth 7]	Triplex capsid protein 2	structural molecule activity	-	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
J [auth b], M [auth 5]	Triplex capsid protein 1	DNA binding binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	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
F [auth S], G [auth T], H [auth W], I [auth X]	Major capsid protein	structural molecule activity	-	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 viral capsid icosahedral viral capsid virion component T=16 icosahedral viral capsid
D [auth n], E [auth o]	Large tegument protein deneddylase	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host ubiquitin-like protein modification symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction	viral capsid 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 viral membrane viral envelope viral capsid 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 viral membrane viral envelope host cell cytoplasm viral tegument
B [auth l], C [auth m]	Capsid vertex component 2	-	biological process involved in interspecies interaction between organisms viral penetration into host nucleus intracellular transport of virus viral process viral life cycle transport of virus biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host biological process involved in interaction with host virion assembly viral genome packaging	host cellular component cellular anatomical structure host cell other organism part viral capsid virion component host intracellular membrane-bounded organelle host intracellular part host cell part host intracellular region host cell nucleus host intracellular organelle
A [auth k]	Capsid vertex component 1	-	cellular component organization organelle organization chromosome organization cellular process cellular component organization or biogenesis	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
P [auth 0], Q [auth 1], R [auth 2], S [auth 3]	IPR009299	Gammaherpesvirus capsid	Family
K [auth c], L [auth d], N [auth 6], O [auth 7]	IPR002690	Herpesvirus capsid protein 2	Family
J [auth b], M [auth 5]	IPR004999	Herpesvirus capsid shell protein 1	Family
F [auth S], G [auth T], H [auth W], I [auth X]	IPR000912	Herpesvirus major capsid protein	Family
F [auth S], G [auth T], H [auth W], I [auth X]	IPR023233	Herpesvirus major capsid protein, upper domain superfamily	Homologous Superfamily
D [auth n], E [auth o]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
D [auth n], E [auth o]	IPR006928	Herpesvirus large tegument protein, USP domain	Domain
D [auth n], E [auth o]	IPR034702	Large tegument protein deneddylase	Family
B [auth l], C [auth m]	IPR002493	Herpesvirus UL25	Family
A [auth k]	IPR007640	Herpesvirus capsid vertex component 1	Family

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.