6PCU | pdb_00006pcu

VP8* of a G2P[4] human rotavirus in complex with scFv antibody 9

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
B	d6pcub_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth E]	d6pcue_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth H]	d6pcuh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6pcua1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)
A	d6pcua2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)
C [auth D]	d6pcud1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)
C [auth D]	d6pcud2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)
E [auth G]	d6pcug1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	automated matches	automated matches	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)
E [auth G]	d6pcug2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Rotavirus A ) [TaxId: 28875 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077032	3000120	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077032	3000120	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8077032	3000120	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)
B	V-set_3	e6pcuB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
D [auth E]	V-set_3	e6pcuE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
F [auth H]	V-set_3	e6pcuH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
A	VP4_haemagglut	e6pcuA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
C [auth D]	VP4_haemagglut	e6pcuD1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)
E [auth G]	VP4_haemagglut	e6pcuG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: VP4_haemagglut	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
C [auth D]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
E [auth G]	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
B, D [auth E], F [auth H]	scFv 9	V-LAMBDA	Homo sapiens (human)	IGLV9-4901, IGLV9-4902, IGLV9-4903, IGLJ201, IGLJ302, IGLJ301	V-DOMAIN V-LAMBDA	IG	FV-HEAVY_LAMBDA	IMGT (202538-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, D [auth E], F [auth H]	Light Chain	IGLV9	Lambda	outer capsid protein vp4	SAbDab (2025-10-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth D], E [auth G]	PF00426	Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain (VP4_haemagglut)	Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain	This entry represents the N-terminal concanavalin-like domain from the VP4 protein of rotavirus.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D [auth E], F [auth H]	Variable domain of antibody scFv9	-	-	-
A, C [auth D], E [auth G]	Outer capsid protein VP4	-	viral process viral life cycle	viral capsid virion component cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth D], E [auth G]	IPR000416	Haemagglutinin outer capsid protein VP4, concanavalin-like domain	Domain
A, C [auth D], E [auth G]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C [auth D], E [auth G]	IPR035330	Rotavirus VP4, membrane interaction domain	Domain
A, C [auth D], E [auth G]	IPR038017	Rotavirus VP4, membrane interaction domain superfamily	Homologous Superfamily

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.