5ZZ8 | pdb_00005zz8

Structure of the Herpes simplex virus type 2 C-capsid with capsid-vertex-specific component

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)
NA [auth r]	Phage_lysozyme	e5zz8r01	A: beta barrels	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: Phage_lysozyme	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], KA [auth D], MA [auth E], OA [auth F], P [auth I], Q [auth J], QA [auth G], R [auth K], S [auth L], T [auth M], U [auth A], V [auth H]	PF04496	Herpesvirus UL35 family (Herpes_UL35)	Herpesvirus UL35 family	-	Family
B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], I [auth Y], K [auth 3], L [auth 2], N [auth x], O [auth y]	PF01802	Herpesvirus VP23 like capsid protein (Herpes_V23)	Herpesvirus VP23 like capsid protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
RA [auth t], YA [auth u]	UL36	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 deNEDDylase activity	viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process viral DNA genome replication primary metabolic process viral life cycle DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process viral genome replication viral process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process proteolysis protein 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	virion component
NA [auth r], PA [auth s]	UL25	-	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
LA [auth q]	UL17	-	cellular component organization organelle organization chromosome organization cellular process cellular component organization or biogenesis	viral capsid virion component
AA [auth l], BA [auth m], CA [auth n], DA [auth o], EA [auth p], AA [auth l], BA [auth m], CA [auth n], DA [auth o], EA [auth p], SA [auth b], TA [auth c], UA [auth d], VA [auth e], W [auth h], WA [auth f], X [auth i], XA [auth g], Y [auth j], Z [auth k]	VP26	-	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
FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], KA [auth D], MA [auth E], OA [auth F], P [auth I], Q [auth J], QA [auth G], R [auth K], S [auth L], T [auth M], U [auth A], V [auth H]	Major capsid protein	structural molecule activity	-	viral capsid icosahedral viral capsid virion component T=16 icosahedral viral capsid
B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], I [auth Y], K [auth 3], L [auth 2], N [auth x], O [auth y]	VP23	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
A [auth Q], D [auth T], G [auth W], J [auth 1], M [auth w]	VP19C	DNA binding binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
RA [auth t], YA [auth u]	IPR005210	Herpesvirus large tegument protein deneddylase	Domain
RA [auth t], YA [auth u]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
RA [auth t], YA [auth u]	IPR006928	Herpesvirus large tegument protein, USP domain	Domain
RA [auth t], YA [auth u]	IPR034702	Large tegument protein deneddylase	Family
NA [auth r], PA [auth s]	IPR002493	Herpesvirus UL25	Family
LA [auth q]	IPR007640	Herpesvirus capsid vertex component 1	Family
AA [auth l], BA [auth m], CA [auth n], DA [auth o], EA [auth p], AA [auth l], BA [auth m], CA [auth n], DA [auth o], EA [auth p], SA [auth b], TA [auth c], UA [auth d], VA [auth e], W [auth h], WA [auth f], X [auth i], XA [auth g], Y [auth j], Z [auth k]	IPR007584	Herpesvirus UL35	Family
FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], KA [auth D], MA [auth E], OA [auth F], P [auth I], Q [auth J], QA [auth G], R [auth K], S [auth L], T [auth M], U [auth A], V [auth H]	IPR000912	Herpesvirus major capsid protein	Family
FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], FA [auth N], GA [auth O], HA [auth P], IA [auth B], JA [auth C], KA [auth D], MA [auth E], OA [auth F], P [auth I], Q [auth J], QA [auth G], R [auth K], S [auth L], T [auth M], U [auth A], V [auth H]	IPR023233	Herpesvirus major capsid protein, upper domain superfamily	Homologous Superfamily
B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], B [auth R], C [auth S], E [auth U], F [auth V], H [auth X], I [auth Y], K [auth 3], L [auth 2], N [auth x], O [auth y]	IPR002690	Herpesvirus capsid protein 2	Family
A [auth Q], D [auth T], G [auth W], J [auth 1], M [auth w]	IPR004999	Herpesvirus capsid shell protein 1	Family

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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.