6XW4 | pdb_00006xw4

Crystal structure of murine norovirus P domain in complex with Nanobody NB-5867

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)
C	d6xw4c1	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	d6xw4c3	Artifacts	Tags	Tags	Tags	C-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
C	d6xw4c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d6xw4d1	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	d6xw4d3	Artifacts	Tags	Tags	Tags	C-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
D	d6xw4d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	alpaca (Vicugna pacos ) [TaxId: 30538 ],	SCOPe (2.08)
A	d6xw4a_	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	d6xw4b_	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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	V-set_8	e6xw4C1	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)
D	V-set_8	e6xw4D1	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)
A	Calici_coat_C_C	e6xw4A1	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	e6xw4B1	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)

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)
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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	capsid protein	SAbDab (2026-01-16)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Nanobody NB-5867	-	-	-
A, B	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	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.