6OKP | pdb_00006okp

B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	gp120 core	8097270	3001390	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	gp120 core	8097270	3001390	SCOP2B (2022-06-29)
D	SCOP2 Family	gp120 core	8097269	4002534	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	gp120 core	8097270	3001390	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Virus ectodomain	8085612	3001628	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus ectodomain	8085612	3001628	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Virus ectodomain	8085612	3001628	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)
F	GP120_2nd	e6okpF2	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
F	GP120_3rd	e6okpF1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
F	GP120_1st	e6okpF3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
E	GP120_2nd	e6okpE3	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
E	GP120_3rd	e6okpE2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
E	GP120_1st	e6okpE1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
D	GP120_2nd	e6okpD2	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
D	GP120_3rd	e6okpD3	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
D	GP120_1st	e6okpD1	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
G [auth K]	V-set_8	e6okpK1	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)
H [auth L]	V-set_3	e6okpL1	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)
N [auth R]	V-set	e6okpR1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
L [auth P]	V-set	e6okpP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
J [auth N]	V-set	e6okpN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
M [auth Q]	V-set_8	e6okpQ1	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)
K [auth O]	V-set_8	e6okpO1	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)
I [auth M]	V-set_8	e6okpM1	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)
C	GP41_1st	e6okpC1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
B	GP41_1st	e6okpB1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
A	GP41_1st	e6okpA1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)

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
G [auth K]	Fab 10-1074, broadly neutralizing antibody	VH	Homo sapiens (human)	IGHV4-5901, IGHV4-5902, IGHV4-5908, IGHV4-408	V-DOMAIN VH	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)
H [auth L]	Fab 10-1074, broadly neutralizing antibody	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLJ201, IGLJ701, IGLJ301, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)
J [auth N], L [auth P], N [auth R]	Fab SF12, broadly neutralizing antibody	L-KAPPA	Homo sapiens (human)	IGKV3-1102, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)
I [auth M], K [auth O], M [auth Q]	Fab SF12, broadly neutralizing antibody	VH-CH1	Homo sapiens (human)	IGHV4-5901, IGHV4-5902, IGHV4-5908, IGHV4-408, IGHJ502, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202604-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth K]	Heavy Chain	IGHV4	-	envelope glycoprotein gp120	SAbDab (2026-02-06)
J [auth N], L [auth P], N [auth R]	Light Chain	IGKV3	Kappa	envelope glycoprotein gp120	SAbDab (2026-02-06)
I [auth M], K [auth O], M [auth Q]	Heavy Chain	IGHV4	-	envelope glycoprotein gp120	SAbDab (2026-02-06)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
G [auth K]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2026-02-06)
H [auth L]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2026-02-06)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, E, F	Envelope glycoprotein gp120	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process 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 plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane
G [auth K]	10-1074 Heavy Chain,10-1074 Heavy Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
H [auth L]	10-1074 Light Chain,10-1074 Light Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
J [auth N], L [auth P], N [auth R]	SF12 Light Chain,SF12 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 extracellular space blood microparticle IgM immunoglobulin complex IgE immunoglobulin complex IgD immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle protein-containing complex IgA immunoglobulin complex immunoglobulin complex cellular anatomical structure extracellular region extracellular space 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
I [auth M], K [auth O], M [auth Q]	SF12 Heavy Chain,SF12 Heavy Chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
A, B, C	Envelope glycoprotein gp41	structural molecule activity	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell membrane organization cellular component organization membrane fusion fusion of virus membrane with host plasma membrane cellular process cellular component organization or biogenesis regulation of localization regulation of biological process cellular localization regulation of cellular process regulation of protein localization positive regulation of receptor clustering biological regulation positive regulation of biological process positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization macromolecule localization receptor clustering positive regulation of protein localization intracellular protein localization regulation of receptor clustering regulation of protein localization to membrane positive regulation of cellular process 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 plasma membrane raft distribution regulation of cellular component organization positive regulation of cellular component organization plasma membrane raft polarization plasma membrane organization membrane raft organization endomembrane system organization membrane raft distribution plasma membrane raft localization membrane raft polarization regulation of plasma membrane raft polarization membrane raft localization regulation of plasma membrane organization positive regulation of plasma membrane raft polarization import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell viral gene expression viral protein processing symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part cellular anatomical structure membrane virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, E, F	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
D, E, F	IPR036377	Gp120 core superfamily	Homologous Superfamily
D, E, F	IPR000328	Retroviral envelope protein GP41-like	Domain
D, E, F	IPR037527	Envelope glycoprotein Gp160	Family
G [auth K]	IPR003597	Immunoglobulin C1-set	Domain
G [auth K]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
G [auth K]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
G [auth K]	IPR013106	Immunoglobulin V-set domain	Domain
G [auth K]	IPR003599	Immunoglobulin domain subtype	Domain
G [auth K]	IPR007110	Immunoglobulin-like domain	Domain
G [auth K]	IPR050380	Immune Recognition and Response Modulators	Family
G [auth K]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
H [auth L]	IPR003597	Immunoglobulin C1-set	Domain
H [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
H [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
H [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
H [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
H [auth L]	IPR007110	Immunoglobulin-like domain	Domain
H [auth L]	IPR050160	Major Histocompatibility Complex/Immunoglobulin	Family
H [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
J [auth N], L [auth P], N [auth R]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
J [auth N], L [auth P], N [auth R]	IPR050380	Immune Recognition and Response Modulators	Family
J [auth N], L [auth P], N [auth R]	IPR003597	Immunoglobulin C1-set	Domain
J [auth N], L [auth P], N [auth R]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
J [auth N], L [auth P], N [auth R]	IPR007110	Immunoglobulin-like domain	Domain
J [auth N], L [auth P], N [auth R]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
I [auth M], K [auth O], M [auth Q]	IPR003597	Immunoglobulin C1-set	Domain
I [auth M], K [auth O], M [auth Q]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
I [auth M], K [auth O], M [auth Q]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
I [auth M], K [auth O], M [auth Q]	IPR013106	Immunoglobulin V-set domain	Domain
I [auth M], K [auth O], M [auth Q]	IPR003599	Immunoglobulin domain subtype	Domain
I [auth M], K [auth O], M [auth Q]	IPR007110	Immunoglobulin-like domain	Domain
I [auth M], K [auth O], M [auth Q]	IPR050380	Immune Recognition and Response Modulators	Family
I [auth M], K [auth O], M [auth Q]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B, C	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A, B, C	IPR036377	Gp120 core superfamily	Homologous Superfamily
A, B, C	IPR000328	Retroviral envelope protein GP41-like	Domain
A, B, C	IPR037527	Envelope glycoprotein Gp160	Family

Pharos: Disease Associations Pharos Homepage Annotation

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