5O04

GII.10 Vietnam 026 norovirus protruding domain in complex with Nanobody Nano-26 and Nano-85

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5o04a_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Norwalk virus ) [TaxId: 11983 ],	SCOPe (2.08)
B	d5o04b_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Norwalk virus ) [TaxId: 11983 ],	SCOPe (2.08)
C [auth E]	d5o04e1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
C [auth E]	d5o04e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
E [auth F]	d5o04f1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
E [auth F]	d5o04f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d5o04d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d5o04d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth C]	d5o04c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth C]	d5o04c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth C]	d5o04c3	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF08435	e5o04A1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF08435	ECOD (1.6)
B	PF08435	e5o04B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: PF08435	ECOD (1.6)
C [auth E]	PF07686	e5o04E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth F]	PF07686	e5o04F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e5o04D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
F [auth C]	PF07686	e5o04C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (4.3.0)
A	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (4.3.0)
B	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth E], E [auth F]	Heavy Chain	IGHV1	-	capsid protein	SAbDab (2024-05-03)
D, F [auth C]	Heavy Chain	IGHV1	-	capsid protein	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00915	Calicivirus coat protein (Calici_coat)	Calicivirus coat protein	-	Family
A, B	PF08435	Calicivirus coat protein C-terminal (Calici_coat_C)	Calicivirus coat protein C-terminal	-	Family

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B	IPR004005	Calicivirus coat protein	Domain
A, B	IPR013643	Calicivirus coat protein C-terminal	Domain
A, B	IPR033703	Picornavirus/Calicivirus coat protein	Domain

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.