2GEF | pdb_00002gef

Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Birnavirus VP4 protease-like	8049479	4006521	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribosomal protein S5 domain 2-like	8053557	3000100	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053557	3000100	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	Birna_VP4	e2gefA1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Birna_VP4	ECOD (develop294)
A	Peptidase_M23	e2gefA2	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Peptidase_M23	ECOD (develop294)
B	Peptidase_M23	e2gefB1	A: alpha bundles	X: amino-terminal domain of OmpATb	H: amino-terminal domain of OmpATb	T: amino-terminal domain of OmpATb	F: Peptidase_M23	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.42.30	Mainly Beta	Roll	Pdz3 Domain		CATH (4.3.0)
A	3.40.50.11300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	2.30.42.30	Mainly Beta	Roll	Pdz3 Domain		CATH (4.3.0)
B	3.40.50.11300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Protease VP4	structural molecule activity peptidase activity serine hydrolase activity catalytic activity, acting on a protein serine-type peptidase activity hydrolase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part viral capsid icosahedral viral capsid T=13 icosahedral viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B	IPR043048	Birnavirus VP3, domain 1	Homologous Superfamily
A, B	IPR002662	Birnavirus VP2 protein	Family
A, B	IPR025775	Birnavirus VP4 protease domain	Domain
A, B	IPR002663	Birnavirus VP3 protein	Family
A, B	IPR043049	Birnavirus VP3, domain 2	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.