6XW7

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5829 and glycochenodeoxycholate (GCDCA)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product 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	d6xw7a1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
A	d6xw7a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
C [auth E]	d6xw7e_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
B	d6xw7b_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
D [auth F]	d6xw7f_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
E [auth C]	d6xw7c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
E [auth C]	d6xw7c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
E [auth C]	d6xw7c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth D]	d6xw7d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth D]	d6xw7d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
F [auth D]	d6xw7d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
G	d6xw7g1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
G	d6xw7g3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
G	d6xw7g2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d6xw7h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
H	d6xw7h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(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	Calici_coat_C_C	e6xw7A1	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: Calici_coat_C_C	ECOD (1.6)
C [auth E]	Calici_coat_C_C	e6xw7E1	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: Calici_coat_C_C	ECOD (1.6)
B	Calici_coat_C_C	e6xw7B1	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: Calici_coat_C_C	ECOD (1.6)
D [auth F]	Calici_coat_C_C	e6xw7F1	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: Calici_coat_C_C	ECOD (1.6)
E [auth C]	V-set_8	e6xw7C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F [auth D]	V-set_8	e6xw7D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
G	V-set_8	e6xw7G1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
H	V-set_12	e6xw7H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	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 (utative)
A	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
C [auth E]	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (utative)
C [auth E]	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
B	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (utative)
B	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)
D [auth F]	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (utative)
D [auth F]	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (utative)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth C], F [auth D], G, H	Heavy Chain	IGHV1	-	capsid protein	SAbDab (2024-12-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth E], D [auth F]	PF08435	Calicivirus coat protein C-terminal (Calici_coat_C)	Calicivirus coat protein C-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth E], D [auth F]	Capsid protein	-	-	virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region
E [auth C], F [auth D], G, H	Nanobody NB-5829	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth E], D [auth F]	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR004005	Calicivirus coat protein	Domain
A, B, C [auth E], D [auth F]	IPR013643	Calicivirus coat protein C-terminal	Domain
A, B, C [auth E], D [auth F]	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 R01GM157729.