5WDU | pdb_00005wdu

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv

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)
Q [auth R]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
L [auth J]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
E [auth Q]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
A [auth G]	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)
U [auth V]	UDPGP	e5wduV1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
P [auth N]	UDPGP	e5wduN1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
K [auth I]	F_bP_aldolase	e5wduI1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: F_bP_aldolase	ECOD (develop294)
T [auth U]	UDPGP	e5wduU1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
O [auth M]	UDPGP	e5wduM1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
J [auth H]	F_bP_aldolase	e5wduH1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: F_bP_aldolase	ECOD (develop294)
S [auth T]	UDPGP	e5wduT1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
N [auth L]	UDPGP	e5wduL1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
I [auth C]	F_bP_aldolase	e5wduC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: F_bP_aldolase	ECOD (develop294)
R [auth S]	UDPGP	e5wduS1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
M [auth K]	UDPGP	e5wduK1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
H [auth B]	F_bP_aldolase	e5wduB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: F_bP_aldolase	ECOD (develop294)
Q [auth R]	UDPGP	e5wduR1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
L [auth J]	UDPGP	e5wduJ1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
G [auth A]	F_bP_aldolase	e5wduA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: F_bP_aldolase	ECOD (develop294)
F [auth W]	UDPGP	e5wduW1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
D [auth O]	UDPGP	e5wduO1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
B [auth D]	V-set	e5wduD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (develop294)
E [auth Q]	UDPGP	e5wduQ1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
C [auth F]	UDPGP	e5wduF1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UDPGP	ECOD (develop294)
A [auth G]	V-set	e5wduG1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	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
K [auth I], P [auth N], U [auth V]	Fab 35O22, neutralizing antibody	L-LAMBDA	Homo sapiens (human)	IGLV2-1402, IGLV2-1802, IGLV2-2301, IGLV2-2302, IGLV2-2303, IGLJ101, IGLC201, IGLC202, IGLC3*04	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
J [auth H], O [auth M], T [auth U]	Fab 35O22, neutralizing antibody	VH-CH1	Homo sapiens (human)	IGHV1-1801, IGHV1-1804, IGHJ101, IGHJ401, IGHJ502, IGHJ402, IGHJ403, IGHG103	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
I [auth C], N [auth L], S [auth T]	Fab PGT122, neutralizing antibody	VH-CH1	Homo sapiens (human)	IGHV4-5902, IGHJ301, IGHG1*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202610-0)
H [auth B], M [auth K], R [auth S]	Fab PGT122, neutralizing antibody	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)
B [auth D], D [auth O], F [auth W]	NIH45-46 scFv, neutralizing antibody	VH	Homo sapiens (human)	IGHV1-202, IGHV1-1801, IGHV1-1804, IGHJ101	V-DOMAIN VH	IG	FV-HEAVY_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
I [auth C], N [auth L], S [auth T]	Heavy Chain	IGHV4	-	envelope glycoprotein gp160	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K [auth I], P [auth N], U [auth V]	bnAb 35O22 Fab light chain	-	-	-
J [auth H], O [auth M], T [auth U]	bnAb 35O22 Fab heavy chain	-	-	-
I [auth C], N [auth L], S [auth T]	bnAb PGT122 Fab heavy chain	-	-	-
H [auth B], M [auth K], R [auth S]	bnAb PGT122 Fab light chain	-	-	-
G [auth A], L [auth J], Q [auth R]	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
B [auth D], D [auth O], F [auth W]	bnAb NIH45-46 scFv	-	-	-
A [auth G], C [auth F], E [auth Q]	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

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

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