4IZJ

Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053556	3000100	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053556	3000100	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053556	3000100	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053556	3000100	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8053556	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	PF01768	e4izjA1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF01768	ECOD (1.6)
A	PF01768	e4izjA2	A: a/b three-layered sandwiches	X: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	H: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: PF01768	ECOD (1.6)
E	PF01768	e4izjE3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF01768	ECOD (1.6)
E	PF01768	e4izjE2	A: a/b three-layered sandwiches	X: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	H: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: PF01768	ECOD (1.6)
D	PF01768	e4izjD3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF01768	ECOD (1.6)
D	PF01768	e4izjD2	A: a/b three-layered sandwiches	X: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	H: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: PF01768	ECOD (1.6)
B	PF01768	e4izjB3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF01768	ECOD (1.6)
B	PF01768	e4izjB2	A: a/b three-layered sandwiches	X: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	H: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: PF01768	ECOD (1.6)
C	PF01768	e4izjC3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: PF01768	ECOD (1.6)
C	PF01768	e4izjC2	A: a/b three-layered sandwiches	X: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	H: C-terminal subdomain in Lon-related proteases catalytic domains (From Topology)	T: C-terminal subdomain in Lon-related proteases catalytic domains	F: PF01768	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.230.110	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
E	3.30.230.110	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
D	3.30.230.110	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
B	3.30.230.110	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)
C	3.30.230.110	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S5	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E	PF01768	Birnavirus VP4 protein (Birna_VP4)	Birnavirus VP4 protein	-	Family
D	PF01768	Birnavirus VP4 protein (Birna_VP4)	Birnavirus VP4 protein	-	Family
B, C	PF01768	Birnavirus VP4 protein (Birna_VP4)	Birnavirus VP4 protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E	Yellowtail Ascites Virus (YAV) VP4 protease	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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	viral capsid virion component intracellular anatomical structure cytoplasm cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region
D	Yellowtail Ascites Virus (YAV) VP4 protease	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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	viral capsid virion component intracellular anatomical structure cytoplasm cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region
B, C	Yellowtail Ascites Virus (YAV) VP4 protease	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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	viral capsid virion component intracellular anatomical structure cytoplasm cellular anatomical entity host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, E	CSO	Parent Component: CYS RESID: AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210
D	CSO	Parent Component: CYS RESID: AA0205 , AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteine sulfenic acid MOD:00210
B, C	CSO	Parent Component: CYS RESID: AA0205 , AA0205 , AA0205 PSI-MOD : L-cysteine sulfenic acid MOD:00210 , L-cysteine sulfenic acid MOD:00210 , L-cysteine sulfenic acid MOD:00210

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 R01GM133198.