6E5P | pdb_00006e5p

Backbone model based on cryo-EM map at 8.5 A of domain-swapped, glycan-reactive, neutralizing antibody 2G12 bound to HIV-1 Env BG505 DS-SOSIP, which was also bound to CD4-binding site antibody VRC03

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I [auth E]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
E [auth A]	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)
J [auth F]	NTP_transf_2	e6e5pF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
H [auth D]	NTP_transf_2	e6e5pD1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
F [auth B]	EipB_like	e6e5pB1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)
X [auth W]	NTP_transf_2	e6e5pW1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
R [auth P]	NTP_transf_2	e6e5pP1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
M [auth J]	EipB_like	e6e5pJ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)
W [auth V]	NTP_transf_2	e6e5pV1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
Q [auth O]	NTP_transf_2	e6e5pO1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
L [auth I]	EipB_like	e6e5pI1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)
I [auth E]	NTP_transf_2	e6e5pE1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
G [auth C]	NTP_transf_2	e6e5pC1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
E [auth A]	EipB_like	e6e5pA1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)
U [auth S]	NTP_transf_2	e6e5pS1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
T [auth R]	NTP_transf_2	e6e5pR1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
P [auth M]	NTP_transf_2	e6e5pM1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
K [auth H]	NTP_transf_2	e6e5pH1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
C [auth 3]	NTP_transf_2	e6e5p31	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
B [auth 2]	EipB_like	e6e5p21	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)
V [auth T]	NTP_transf_2	e6e5pT1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
S [auth Q]	NTP_transf_2	e6e5pQ1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
O [auth L]	NTP_transf_2	e6e5pL1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
N [auth K]	NTP_transf_2	e6e5pK1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
D [auth 4]	NTP_transf_2	e6e5p41	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: NTP_transf_2	ECOD (v294.1)
A [auth 1]	EipB_like	e6e5p11	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: EipB_like	ECOD (v294.1)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
M [auth J], R [auth P], X [auth W]	Light Chain	IGKV3	Kappa	envelope glycoprotein gp120	SAbDab (2026-03-27)
A [auth 1], D [auth 4], N [auth K], O [auth L], S [auth Q], A [auth 1], D [auth 4], N [auth K], O [auth L], S [auth Q], V [auth T]	Light Chain	IGKV1	Kappa	polysaccharide, envelope glycoprotein gp120	SAbDab (2026-03-27)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
F [auth B], H [auth D], J [auth F]	Envelope glycoprotein gp160	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
M [auth J], R [auth P], X [auth W]	VRC03 Light chain	-	-	-
L [auth I], Q [auth O], W [auth V]	VRC03 heavy chain	-	-	-
E [auth A], G [auth C], I [auth E]	Envelope glycoprotein gp120	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
B [auth 2], C [auth 3], K [auth H], P [auth M], T [auth R], B [auth 2], C [auth 3], K [auth H], P [auth M], T [auth R], U [auth S]	2G12 heavy chain	-	-	-
A [auth 1], D [auth 4], N [auth K], O [auth L], S [auth Q], A [auth 1], D [auth 4], N [auth K], O [auth L], S [auth Q], V [auth T]	2G12 Light chain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
F [auth B], H [auth D], J [auth F]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
F [auth B], H [auth D], J [auth F]	IPR036377	Gp120 core superfamily	Homologous Superfamily
F [auth B], H [auth D], J [auth F]	IPR000328	Retroviral envelope protein GP41-like	Domain
F [auth B], H [auth D], J [auth F]	IPR037527	Envelope glycoprotein Gp160	Family
E [auth A], G [auth C], I [auth E]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
E [auth A], G [auth C], I [auth E]	IPR036377	Gp120 core superfamily	Homologous Superfamily
E [auth A], G [auth C], I [auth E]	IPR000328	Retroviral envelope protein GP41-like	Domain
E [auth A], G [auth C], I [auth E]	IPR037527	Envelope glycoprotein Gp160	Family