6UDK | pdb_00006udk

HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Thera-SAbDab Antibody Annotation
Protein Family 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)
R [auth Q]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
Q [auth J]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
P [auth C]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
C [auth R]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
B [auth K]	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)
R [auth Q]	GP41_1st	e6udkQ1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
Q [auth J]	GP41_1st	e6udkJ1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
P [auth C]	GP41_1st	e6udkC1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: GP41_1st	ECOD (1.6)
O [auth L]	V-set	e6udkL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
M [auth E]	V-set	e6udkE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
K [auth N]	V-set	e6udkN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
N [auth H]	V-set_8	e6udkH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
L [auth D]	V-set_8	e6udkD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
J [auth M]	V-set_8	e6udkM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
I [auth P]	V-set_3	e6udkP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
G [auth I]	V-set_3	e6udkI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
E [auth B]	V-set_3	e6udkB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_3	ECOD (1.6)
H [auth O]	V-set_8	e6udkO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
F	V-set_8	e6udkF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
D [auth A]	V-set_8	e6udkA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth R]	GP120_2nd	e6udkR1	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
C [auth R]	GP120_3rd	e6udkR2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
C [auth R]	GP120_1st	e6udkR3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
B [auth K]	GP120_2nd	e6udkK2	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
B [auth K]	GP120_3rd	e6udkK1	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
B [auth K]	GP120_1st	e6udkK3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)
A [auth G]	GP120_2nd	e6udkG1	A: beta barrels	X: V1/V2 domain in HIV gp120 (From Topology)	H: V1/V2 domain in HIV gp120 (From Topology)	T: V1/V2 domain in HIV gp120	F: GP120_2nd	ECOD (1.6)
A [auth G]	GP120_3rd	e6udkG2	A: a+b two layers	X: Ribosomal protein L31e-like	H: Ribosomal protein L31e/gp120 outer domain (From Topology)	T: Ribosomal protein L31e/gp120 outer domain	F: GP120_3rd	ECOD (1.6)
A [auth G]	GP120_1st	e6udkG3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: GP120_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
L [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
J [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

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 N], M [auth E], O [auth L]	Fab 1-55, anti-HIV, broadly neutralizing	null	Homo sapiens (human)	-	-	IG	FAB-GAMMA-1_KAPPA	IMGT (202540-0)
J [auth M], L [auth D], N [auth H]	Fab 1-55, anti-HIV, broadly neutralizing	null	Homo sapiens (human)	-	-	IG	FAB-GAMMA-1_KAPPA	IMGT (202540-0)
E [auth B], G [auth I], I [auth P]	Fab 10-1074, anti-HIV, broadly neutralizing	L-LAMBDA	Homo sapiens (human)	IGLV3-2101, IGLV3-2104, IGLJ201, IGLJ701, IGLJ301, IGLC201, IGLC202, IGLC304	V-DOMAIN V-LAMBDA, C-DOMAIN C-LAMBDA	IG	FAB-GAMMA-1_LAMBDA	IMGT (202540-0)
D [auth A], F, H [auth O]	Fab 10-1074, anti-HIV, broadly neutralizing	1C-LIKE	Homo sapiens (human)	IGHV4-5901, IGHV4-5908, IGHV4-5913, IGHJ604, IGHG103, IGHG108, IGHG1*06	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_LAMBDA	IMGT (202540-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
K [auth N], M [auth E], O [auth L]	Light Chain	IGKV3	Kappa	rc1 variant of hiv-1 env glycoprotein gp120	SAbDab (2025-10-17)
D [auth A], F, H [auth O]	Heavy Chain	IGHV4	-	rc1 variant of hiv-1 env glycoprotein gp120	SAbDab (2025-10-17)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
E [auth B], G [auth I], I [auth P]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2025-10-17)
D [auth A], F, H [auth O]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2025-10-17)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
P [auth C], Q [auth J], R [auth Q]	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family
K [auth N], M [auth E], O [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
J [auth M], L [auth D], N [auth H]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
E [auth B], G [auth I], I [auth P]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
D [auth A], F, H [auth O]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
A [auth G], B [auth K], C [auth R]	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell s ...	The envelope glycoprotein Gp160 of HIV1 is cleaved into the surface protein Gp120 and the transmembrane protein Gp41. The entry of HIV requires interaction of viral GP120 with the CD4 glycoprotein (Swiss:P01730) and a chemokine receptor on the cell surface [1]. Gp160 us proteolytically cleaved n the trans-Golgi and activated by cellular furin or furin-like proteases to produce gp120 and gp41 [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
P [auth C], Q [auth J], R [auth Q]	RC1 variant of HIV-1 Env 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
K [auth N], M [auth E], O [auth L]	1-55 Fab Light 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
J [auth M], L [auth D], N [auth H]	1-55 Fab Heavy 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 B], G [auth I], I [auth P]	10-1074 Fab Light 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
D [auth A], F, H [auth O]	10-1074 Fab Heavy 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
A [auth G], B [auth K], C [auth R]	RC1 variant of HIV-1 Env 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
P [auth C], Q [auth J], R [auth Q]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
P [auth C], Q [auth J], R [auth Q]	IPR036377	Gp120 core superfamily	Homologous Superfamily
P [auth C], Q [auth J], R [auth Q]	IPR000328	Retroviral envelope protein GP41-like	Domain
P [auth C], Q [auth J], R [auth Q]	IPR037527	Envelope glycoprotein Gp160	Family
K [auth N], M [auth E], O [auth L]	IPR003597	Immunoglobulin C1-set	Domain
K [auth N], M [auth E], O [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
K [auth N], M [auth E], O [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
K [auth N], M [auth E], O [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
K [auth N], M [auth E], O [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
K [auth N], M [auth E], O [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
K [auth N], M [auth E], O [auth L]	IPR007110	Immunoglobulin-like domain	Domain
K [auth N], M [auth E], O [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
J [auth M], L [auth D], N [auth H]	IPR003597	Immunoglobulin C1-set	Domain
J [auth M], L [auth D], N [auth H]	IPR050199	Immunoglobulin Heavy Variable	Family
J [auth M], L [auth D], N [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
J [auth M], L [auth D], N [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
J [auth M], L [auth D], N [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
J [auth M], L [auth D], N [auth H]	IPR003599	Immunoglobulin domain subtype	Domain
J [auth M], L [auth D], N [auth H]	IPR007110	Immunoglobulin-like domain	Domain
J [auth M], L [auth D], N [auth H]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
E [auth B], G [auth I], I [auth P]	IPR003597	Immunoglobulin C1-set	Domain
E [auth B], G [auth I], I [auth P]	IPR050150	Immunoglobulin Variable Light Chain	Family
E [auth B], G [auth I], I [auth P]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
E [auth B], G [auth I], I [auth P]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
E [auth B], G [auth I], I [auth P]	IPR013106	Immunoglobulin V-set domain	Domain
E [auth B], G [auth I], I [auth P]	IPR003599	Immunoglobulin domain subtype	Domain
E [auth B], G [auth I], I [auth P]	IPR007110	Immunoglobulin-like domain	Domain
E [auth B], G [auth I], I [auth P]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
D [auth A], F, H [auth O]	IPR003597	Immunoglobulin C1-set	Domain
D [auth A], F, H [auth O]	IPR050199	Immunoglobulin Heavy Variable	Family
D [auth A], F, H [auth O]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth A], F, H [auth O]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth A], F, H [auth O]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth A], F, H [auth O]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth A], F, H [auth O]	IPR007110	Immunoglobulin-like domain	Domain
D [auth A], F, H [auth O]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A [auth G], B [auth K], C [auth R]	IPR000777	Human immunodeficiency virus 1, envelope glycoprotein Gp120	Domain
A [auth G], B [auth K], C [auth R]	IPR036377	Gp120 core superfamily	Homologous Superfamily
A [auth G], B [auth K], C [auth R]	IPR000328	Retroviral envelope protein GP41-like	Domain
A [auth G], B [auth K], C [auth R]	IPR037527	Envelope glycoprotein Gp160	Family