6ODM | pdb_00006odm

Herpes simplex virus type 1 (HSV-1) portal vertex-adjacent capsid/CATC, asymmetric unit

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
M [auth G]	Sel1	e6odmG01	A: a/b three-layered sandwiches	X: Rossmann-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Sel1	ECOD (v294.1)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
O, P [auth B]	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 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
M [auth G], N [auth K]	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
L [auth C]	Capsid vertex component 1	-	cellular component organization organelle organization chromosome organization cellular process cellular component organization or biogenesis	viral capsid virion component
J [auth 6], K [auth 7], R [auth H], S [auth A]	Triplex capsid protein 2	structural molecule activity	-	viral capsid virion component
I [auth 5], Q [auth D]	Triplex capsid protein 1	DNA binding binding nucleic acid binding	virion assembly viral process viral capsid assembly viral life cycle	viral capsid virion component
E [auth L], F [auth P], G [auth E], H [auth F]	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
A [auth T], B [auth W], C [auth S], D [auth X]	Major capsid protein	structural molecule activity	-	viral capsid icosahedral viral capsid virion component T=16 icosahedral viral capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
O, P [auth B]	IPR005210	Herpesvirus large tegument protein deneddylase	Domain
O, P [auth B]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
O, P [auth B]	IPR006928	Herpesvirus large tegument protein, USP domain	Domain
O, P [auth B]	IPR034702	Large tegument protein deneddylase	Family
M [auth G], N [auth K]	IPR002493	Herpesvirus UL25	Family
L [auth C]	IPR007640	Herpesvirus capsid vertex component 1	Family
J [auth 6], K [auth 7], R [auth H], S [auth A]	IPR002690	Herpesvirus capsid protein 2	Family
I [auth 5], Q [auth D]	IPR004999	Herpesvirus capsid shell protein 1	Family
E [auth L], F [auth P], G [auth E], H [auth F]	IPR007584	Herpesvirus UL35	Family
A [auth T], B [auth W], C [auth S], D [auth X]	IPR000912	Herpesvirus major capsid protein	Family
A [auth T], B [auth W], C [auth S], D [auth X]	IPR023233	Herpesvirus major capsid protein, upper domain 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.