9NBY | pdb_00009nby

AMC008 v4.2 SOSIP Env trimer in complex with PGT121, VRC01 and 3BC315 Fabs

External Resource: Annotation

Domain Annotation: ECOD Classification
Thera-SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
E [auth K]	Beta-Casp	e9nbyK1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
K [auth Q]	Beta-Casp	e9nbyQ1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
D [auth J]	Beta-Casp	e9nbyJ1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
H [auth N]	Beta-Casp	e9nbyN1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
I [auth O]	Beta-Casp	e9nbyO1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
N [auth T]	Beta-Casp	e9nbyT1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
C [auth I]	Beta-Casp	e9nbyI1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
G [auth M]	Beta-Casp	e9nbyM1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
J [auth P]	Beta-Casp	e9nbyP1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
L [auth R]	Beta-Casp	e9nbyR1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)
F [auth L]	Beta-Casp	e9nbyL1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: Beta-Casp	ECOD (v295)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
A [auth G], E [auth K], K [auth Q]	Elipovimab	HIV-1 gp120	Therapeutic SAbDab (2026-06-26)
B [auth H], F [auth L], L [auth R]	Elipovimab	HIV-1 gp120	Therapeutic SAbDab (2026-06-26)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], E [auth K], K [auth Q]	PGT121 Fab light chain	-	-	-
D [auth J], H [auth N], I [auth O]	VRC01 Fab light chain	-	-	-
P [auth F], R [auth B], T [auth D]	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 import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization vesicle-mediated transport biological process involved in interaction with host biological process involved in symbiotic interaction localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host cellular process clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host defense response symbiont-mediated perturbation of host process modulation of process of another organism	virion component viral membrane viral envelope host cell plasma membrane host cellular component cellular anatomical structure host cell part host cell membrane other organism part virion membrane
O [auth E], Q [auth A], S [auth C]	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
N [auth T]	3BC315 Fab light chain	-	-	-
M [auth S]	3BC315 Fab heavy chain	-	-	-
C [auth I], G [auth M], J [auth P]	VRC01 Fab heavy chain	-	-	-
B [auth H], F [auth L], L [auth R]	PGT121 Fab heavy chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
P [auth F], R [auth B], T [auth D]	IPR000328	Retroviral envelope protein GP41-like	Domain
O [auth E], Q [auth A], S [auth C]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
O [auth E], Q [auth A], S [auth C]	IPR036377	Gp120 core superfamily	Homologous Superfamily
O [auth E], Q [auth A], S [auth C]	IPR000328	Retroviral envelope protein GP41-like	Domain
O [auth E], Q [auth A], S [auth C]	IPR037527	Envelope glycoprotein Gp160	Family

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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.