5VJ6 | pdb_00005vj6

BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	gp120 core	8080371	3001390	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	GP41_1st	e5vj6B1	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)
C	GP41_1st	e5vj6C1	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	e5vj6A1	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)
F	GP120_2nd	e5vj6F2	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	e5vj6F3	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	e5vj6F1	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	e5vj6E3	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	e5vj6E1	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	e5vj6E2	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	e5vj6D3	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	e5vj6D2	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	e5vj6D1	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 H]	C1-set_1	e5vj6H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
G [auth H]	V-set_12	e5vj6H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
L [auth Q]	C1-set_1	e5vj6Q1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
L [auth Q]	V-set_12	e5vj6Q2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J [auth O]	C1-set_1	e5vj6O2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
J [auth O]	V-set_12	e5vj6O1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
H [auth M]	C1-set_1	e5vj6M1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
H [auth M]	V-set_12	e5vj6M2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
K [auth P]	C1-set_4	e5vj6P2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
K [auth P]	V-set	e5vj6P1	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 R]	C1-set_4	e5vj6R1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
M [auth R]	V-set	e5vj6R2	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)
I [auth N]	C1-set_4	e5vj6N2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
I [auth N]	V-set	e5vj6N1	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)
N [auth L]	C1-set	e5vj6L1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set	ECOD (1.6)
N [auth L]	V-set_3	e5vj6L2	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)

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 H]	Fab PG9, broadly neutralizing	VH	Homo sapiens (human)	IGHV3-3002, IGHV3-3003, IGHV3-3006, IGHV3-3012, IGHV3-3019, IGHV3-3301, IGHV3-3304, IGHV3-3305, IGHV3-30-5*02	V-DOMAIN VH	IG	FAB-GAMMA-1_LAMBDA	IMGT (202605-0)
H [auth M], J [auth O], L [auth Q]	Fab 8ANC195, broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV1-6901, IGHV1-6904, IGHV1-6906, IGHV1-6909, IGHV1-6910, IGHV1-6911, IGHV1-6912, IGHV1-6913, IGHV1-6914, IGHV1-69D01, IGHV1-6915, IGHV1-6917, IGHJ501, IGHG103, IGHG108, IGHG106	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202605-0)
I [auth N], K [auth P], M [auth R]	Fab 8ANC195, broadly neutralizing	L-KAPPA	Homo sapiens (human)	IGKV1-501, IGKV1-502, IGKV1-503, IGKJ101, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202605-0)
N [auth L]	Fab PG9, broadly neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV2-1401, IGLJ101, IGLJ201, IGLJ302, IGLJ301, IGLC303	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202605-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
G [auth H]	Heavy Chain	IGHV3	-	envelope glycoprotein gp160	SAbDab (2026-02-06)
I [auth N], K [auth P], M [auth R]	Light Chain	IGKV1	Kappa	envelope glycoprotein gp160, envelope glycoprotein gp160 \| envelope glycoprotein gp160	SAbDab (2026-02-06)
N [auth L]	Light Chain	IGLV2	Lambda	envelope glycoprotein gp160	SAbDab (2026-02-06)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Envelope glycoprotein gp160	structural molecule activity identical protein binding protein binding binding	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
D, E, F	Envelope glycoprotein gp160	structural molecule activity identical protein binding protein binding binding	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 H]	PG9 Fab 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 M], J [auth O], L [auth Q]	8ANC195 Fab 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
I [auth N], K [auth P], M [auth R]	8ANC195 Fab 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
N [auth L]	PG9 Fab 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

InterPro: Protein Family Classification InterPro Database Homepage

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