6XW7 | pdb_00006xw7

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
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)
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)
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)
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)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	Cation_ATPase	e6xw7H1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
G	Cation_ATPase	e6xw7G1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
F [auth D]	Cation_ATPase	e6xw7D1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
E [auth C]	Cation_ATPase	e6xw7C1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
D [auth F]	Cation_ATPase	e6xw7F1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
C [auth E]	Cation_ATPase	e6xw7E1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
B	Cation_ATPase	e6xw7B1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)
A	Cation_ATPase	e6xw7A1	A: alpha bundles	X: Immunoglobulin-like beta-sandwich	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Cation_ATPase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

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 (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C], F [auth D], G, H	Nanobody NB-5829	-	-	-
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 other organism part

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.