4JO1 | pdb_00004jo1

Crystal structure of rabbit mAb R56 Fab in complex with V3 crown of HIV-1 JR-FL gp120

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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)
B [auth H]	d4jo1h_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
E [auth I]	d4jo1i_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
A [auth L]	d4jo1l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)
D [auth M]	d4jo1m1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	rabbit (Oryctolagus cuniculus ) [TaxId: 9986 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth H]	PAZ	e4jo1H1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: PAZ	ECOD (v294.1)
E [auth I]	PAZ	e4jo1I1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: PAZ	ECOD (v294.1)
A [auth L]	PAZ	e4jo1L1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: PAZ	ECOD (v294.1)
D [auth M]	PAZ	e4jo1M1	A: a/b three-layered sandwiches	X: immunoglobulin/albumin-binding domain-like	H: EGF-related	T: Complement control module/SCR domain	F: PAZ	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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 [auth H], E [auth I]	R56 Fab, anti-gp120 [HIV-1]	VH-CH1	Oryctolagus cuniculus (rabbit)	IGHV1S4001, IGHJ601, IGHG01, IGHG05, IGHG*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)
A [auth L], D [auth M]	R56 Fab, anti-gp120 [HIV-1]	L-KAPPA	Oryctolagus cuniculus (rabbit)	IGKV1S501, IGKJ1-202, IGKJ1-201, IGKC101	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202611-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H], E [auth I]	Heavy Chain	IGHV1	-	gp120	SAbDab (2026-03-27)
A [auth L], D [auth M]	Light Chain	IGKV1	Kappa	gp120	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth P], F [auth Q]	gp120	-	viral process membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	virion component viral membrane viral envelope virion membrane
B [auth H], E [auth I]	monoclonal anti-HIV-1 gp120 V3 antibody R56 heavy chain	-	-	-
A [auth L], D [auth M]	monoclonal anti-HIV-1 gp120 V3 antibody R56 light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth P], F [auth Q]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
C [auth P], F [auth Q]	IPR036377	Gp120 core 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.