6NC3 | pdb_00006nc3

AMC011 v4.2 SOSIP Env trimer in complex with fusion peptide targeting antibody VRC34 fragment antigen binding

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
V [auth N]	SCOP2B Superfamily	Virus ectodomain	8099952	3001628	SCOP2B (2022-06-29)
R [auth M]	SCOP2B Superfamily	Virus ectodomain	8099952	3001628	SCOP2B (2022-06-29)
N [auth K]	SCOP2B Superfamily	Virus ectodomain	8099952	3001628	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Virus ectodomain	8099952	3001628	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	Virus ectodomain	8099952	3001628	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Virus ectodomain	8099952	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)
X	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3X1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
T [auth W]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3W1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
P [auth V]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3V1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
L [auth U]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3U1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
H [auth T]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3T1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
D [auth L]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3L1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
W [auth S]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3S1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
S [auth R]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3R1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
O [auth Q]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3Q1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
K [auth P]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3P1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
G [auth O]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3O1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
C [auth H]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3H1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
V [auth N]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3N1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
R [auth M]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3M1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
N [auth K]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3K1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
J	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3J1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
F [auth I]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3I1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
B	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3B1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
U [auth G]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3G1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
Q [auth F]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3F1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
M [auth E]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3E1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
I [auth D]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3D1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
E [auth C]	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3C1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	ECOD (develop294)
A	ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	e6nc3A1	A: alpha bundles	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANAPC4_WD40, Beta-prop_WDR36-Utp21_1st	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 L], H [auth T], L [auth U], P [auth V], T [auth W], D [auth L], H [auth T], L [auth U], P [auth V], T [auth W], X	mAb VRC34.01	L-KAPPA	Homo sapiens (human)	IGKV1-901, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)
C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], W [auth S]	mAb VRC34.01	VH-CH1	Homo sapiens (human)	IGHV1-202, IGHJ601, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L], H [auth T], L [auth U], P [auth V], T [auth W], D [auth L], H [auth T], L [auth U], P [auth V], T [auth W], X	Light Chain	IGKV1	Kappa	hiv-1 env amc011 v4.2 sosip gp41 \| hiv-1 env amc011 v4.2 sosip gp120	SAbDab (2026-03-20)
C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], W [auth S]	Heavy Chain	IGHV1	-	hiv-1 env amc011 v4.2 sosip gp41 \| hiv-1 env amc011 v4.2 sosip gp120	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L], H [auth T], L [auth U], P [auth V], T [auth W], D [auth L], H [auth T], L [auth U], P [auth V], T [auth W], X	Monoclonal antibody VRC34.01 fragment antigen binding light chain	-	-	-
C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], C [auth H], G [auth O], K [auth P], O [auth Q], S [auth R], W [auth S]	Monoclonal antibody VRC34.01 fragment antigen binding heavy chain	-	-	-
B, F [auth I], J, N [auth K], R [auth M], B, F [auth I], J, N [auth K], R [auth M], V [auth N]	HIV-1 Env AMC011 v4.2 SOSIP 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	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
A, E [auth C], I [auth D], M [auth E], Q [auth F], A, E [auth C], I [auth D], M [auth E], Q [auth F], U [auth G]	HIV-1 Env AMC011 v4.2 SOSIP gp120	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, F [auth I], J, N [auth K], R [auth M], B, F [auth I], J, N [auth K], R [auth M], V [auth N]	IPR000328	Retroviral envelope protein GP41-like	Domain

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.

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