5D9Q | pdb_00005d9q

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46

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)
A [auth G]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
K [auth J]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
G [auth C]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	Virus ectodomain	8085614	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)
A [auth G]	AMP-binding,ACAS_N	e5d9qG1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
F [auth A]	AMP-binding,ACAS_N	e5d9qA1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
K [auth J]	AMP-binding,ACAS_N	e5d9qJ1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
B	AMP-binding,ACAS_N	e5d9qB1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
G [auth C]	AMP-binding,ACAS_N	e5d9qC1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
L [auth K]	AMP-binding,ACAS_N	e5d9qK1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
D [auth H]	AMP-binding,ACAS_N	e5d9qH1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
I [auth F]	AMP-binding,ACAS_N	e5d9qF1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
N	AMP-binding,ACAS_N	e5d9qN1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
E [auth D]	AMP-binding,ACAS_N	e5d9qD1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
J [auth I]	AMP-binding,ACAS_N	e5d9qI1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
O	AMP-binding,ACAS_N	e5d9qO1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
C [auth L]	AMP-binding,ACAS_N	e5d9qL1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
H [auth E]	AMP-binding,ACAS_N	e5d9qE1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)
M	AMP-binding,ACAS_N	e5d9qM1	A: alpha bundles	X: omega toxin-like	H: omega toxin-related	T: omega toxin-related	F: AMP-binding,ACAS_N	ECOD (develop294)

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
D [auth H], I [auth F], N	PGT122 mAb, anti-gp120 [HIV-1], broadly neutralizing	VH-CH1	Homo sapiens (human)	IGHV4-5902, IGHJ301, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
E [auth D], J [auth I], O	NIH45-46 scFv	SCFV-HEAVY-KAPPA	Homo sapiens (human)	IGHV1-202, IGHV1-1801, IGHV1-1804, IGHJ101, IGKV3-1101, IGKV3-1102, IGKV3D-1102, IGKJ101	V-DOMAIN VH, V-DOMAIN V-KAPPA	IG	SCFV-HEAVY-KAPPA	IMGT (202610-0)
C [auth L], H [auth E], M	PGT122 mAb, anti-gp120 [HIV-1], broadly neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLV3-2102, IGLJ302, IGLC303	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth H], I [auth F], N	Heavy Chain	IGHV4	-	envelope glycoprotein gp120	SAbDab (2026-03-20)
C [auth L], H [auth E], M	Light Chain	IGLV3	Lambda	envelope glycoprotein gp120	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], F [auth A], K [auth J]	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, G [auth C], L [auth K]	Envelope glycoprotein gp41	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 [auth H], I [auth F], N	PGT122 heavy chain,IgG H 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
E [auth D], J [auth I], O	NIH45-46 single chain Fv	-	-	-
C [auth L], H [auth E], M	PGT122 light chain,Ig lambda-3 chain C regions	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E [auth D], J [auth I], O	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.