3OZ9 | pdb_00003oz9

Crystal Structure of anti-gp41 Fab NC-1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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 [auth H]	d3oz9h1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ], (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d3oz9h2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mus musculus ) [TaxId: 10090 ], (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d3oz9l2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ], (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A [auth L]	d3oz9l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ], (Mus musculus ) [TaxId: 10090 ],	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]	PP-binding	e3oz9H1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Ankyrin repeat	T: Ankyrin repeat	F: PP-binding	ECOD (v294.1)
A [auth L]	PP-binding	e3oz9L1	A: a/b three-layered sandwiches	X: Repetitive alpha hairpins	H: Ankyrin repeat	T: Ankyrin repeat	F: PP-binding	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)
A [auth L]	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]	Fab NC-1, anti-gp41 [HIV-1]	VH-CH1	Mus musculus (house mouse)	IGHV1-901, IGHJ301, IGHG2A01, IGHG2A02, IGHG2B01, IGHG2B02, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202612-0)
A [auth L]	Fab NC-1, anti-gp41 [HIV-1]	L-KAPPA	Mus musculus (house mouse)	IGKV4-8001, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202612-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV1	-	-	SAbDab (2026-03-27)
A [auth L]	Light Chain	IGKV4	Kappa	-	SAbDab (2026-03-27)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth H]	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
B [auth H]	Fab NC-1 IgG2a heavy chain	protein-containing complex binding protein binding binding signaling receptor binding immunoglobulin receptor binding Fc-gamma receptor I complex binding antigen binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response response to stimulus positive regulation of biological process positive regulation of response to stimulus complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway regulation of biological process immune response biological regulation immunoglobulin mediated immune response adaptive immune response immune effector process regulation of response to stimulus immune system process B cell mediated immunity regulation of immune response activation of immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	protein-containing complex cellular anatomical structure extracellular region extracellular protein-containing complex immunoglobulin complex, circulating immunoglobulin complex IgG immunoglobulin complex
A [auth L]	Fab NC-1 kappa light chain	cation binding ion binding binding metal ion binding small molecule binding	response to stimulus immune response immune system process adaptive immune response	cellular anatomical structure extracellular region cell periphery plasma membrane membrane protein-containing complex immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H]	IPR007110	Immunoglobulin-like domain	Domain
B [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
A [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A [auth L]	IPR003597	Immunoglobulin C1-set	Domain
A [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
A [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
A [auth L]	IPR007110	Immunoglobulin-like domain	Domain
A [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

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.