3RU8 | pdb_00003ru8

Structure of an HIV epitope scaffold in complex with neutralizing antibody b12 Fab

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth X]	d3ru8x1	Alpha and beta proteins (a/b)	7-stranded beta/alpha barrel	Glycosyl hydrolases family 6, cellulases	Glycosyl hydrolases family 6, cellulases	automated matches	(Human immunodeficiency virus ) [TaxId: 12721 ], (synthetic construct ) [TaxId: 32630 ], (Thermobifida fusca ) [TaxId: 2021 ],	SCOPe (2.08)
A [auth X]	d3ru8x2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Human immunodeficiency virus ) [TaxId: 12721 ], (synthetic construct ) [TaxId: 32630 ], (Thermobifida fusca ) [TaxId: 2021 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091527	3000071	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)
C [auth L]	HRM	e3ru8L1	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: HRM	ECOD (v294.1)
B [auth H]	HRM	e3ru8H1	A: a/b three-layered sandwiches	X: Hormone receptor domain (HRM, Pfam 02793)	H: Hormone receptor domain (HRM, Pfam 02793)	T: Hormone receptor domain (HRM, Pfam 02793)	F: HRM	ECOD (v294.1)
A [auth X]	PIN	e3ru8X1	A: a/b three-layered sandwiches	X: Baculovirus p35 protein-related	H: HIT-related	T: HIT-related	F: PIN	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [auth X]	3.20.20.40	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	1, 4-beta cellobiohydrolase	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
C [auth L]	b12 mAb, anti-gp120 CD4 binding site (CD4bs) [HIV-1],	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)
B [auth H]	b12 mAb, anti-gp120 CD4 binding site (CD4bs) [HIV-1],	VH-CH1	Homo sapiens (human)	IGHV1-301, IGHJ603, IGHG101, IGHG102, IGHG1*04	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth L]	Light Chain	IGKV3	Kappa	epitope scaffold 2bodx43	SAbDab (2026-03-27)
B [auth H]	Heavy Chain	IGHV1	-	epitope scaffold 2bodx43	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth L]	Antibody b12, Light Chain	binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway B cell receptor signaling pathway biological regulation regulation of response to stimulus regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response	protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane IgG immunoglobulin complex
B [auth H]	Antibody b12, Heavy Chain	-	-	-
A [auth X]	Epitope Scaffold 2bodx43	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth L]	IPR050380	Immune Recognition and Response Modulators	Family
C [auth L]	IPR003597	Immunoglobulin C1-set	Domain
C [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth L]	IPR007110	Immunoglobulin-like domain	Domain
C [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth L]	Pharos: P01834	recurrent infections associated with rare immunoglobulin isotypes deficiency myositis dysgammaglobulinemia Hepatomegaly acquired idiopathic inflammatory myopathy selective IgG immunodeficiency

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.