Annotations: 6UDK

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
C [auth R]	SCOP2B Superfamily	gp120 core	8080371	3001390	SCOP2B (2022-06-29)
P [auth C]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
Q [auth J]	SCOP2B Superfamily	Virus ectodomain	8085614	3001628	SCOP2B (2022-06-29)
R [auth Q]	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)
B [auth K]	PF00516	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: PF00516	ECOD (1.6)
B [auth K]	PF00516	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: PF00516	ECOD (1.6)
B [auth K]	PF00516	e6udkK3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
A [auth G]	PF00516	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: PF00516	ECOD (1.6)
A [auth G]	PF00516	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: PF00516	ECOD (1.6)
A [auth G]	PF00516	e6udkG3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
C [auth R]	PF00516	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: PF00516	ECOD (1.6)
C [auth R]	PF00516	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: PF00516	ECOD (1.6)
C [auth R]	PF00516	e6udkR3	A: a+b two layers	X: gp120 inner domain (From Topology)	H: gp120 inner domain (From Topology)	T: gp120 inner domain	F: PF00516	ECOD (1.6)
F	PF07686	e6udkF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
H [auth O]	PF07686	e6udkO1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D [auth A]	PF07686	e6udkA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
G [auth I]	PF07686	e6udkI1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
I [auth P]	PF07686	e6udkP1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
E [auth B]	PF07686	e6udkB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
J [auth M]	PF07686	e6udkM1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
L [auth D]	PF07686	e6udkD1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
N [auth H]	PF07686	e6udkH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
K [auth N]	PF07686	e6udkN1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
M [auth E]	PF07686	e6udkE1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
O [auth L]	PF07686	e6udkL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
P [auth C]	PF00517	e6udkC1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)
Q [auth J]	PF00517	e6udkJ1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)
R [auth Q]	PF00517	e6udkQ1	A: a+b duplicates or obligate multimers	X: MPER trimer (From Topology)	H: MPER trimer (From Topology)	T: MPER trimer	F: PF00517	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J [auth M]	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)
N [auth H]	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
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 (202418-0)
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 (202418-0)
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 (202418-0)
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 (202418-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth A], F, H [auth O]	Heavy Chain	IGHV4	-	rc1 variant of hiv-1 env glycoprotein gp120	SAbDab (2024-05-10)
K [auth N], M [auth E], O [auth L]	Light Chain	IGKV3	Kappa	rc1 variant of hiv-1 env glycoprotein gp120	SAbDab (2024-05-10)

Thera-SAbDab Antibody Annotation Thera-SAbDab Database Homepage

Chain	Name	Target	Provenance Source
D [auth A], F, H [auth O]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2024-05-10)
E [auth B], G [auth I], I [auth P]	Zinlirvimab	HIV-1 gp120 V3	Therapeutic SAbDab (2024-05-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth G], B [auth K], C [auth R]	PF00516	Envelope glycoprotein GP120 (GP120)	Envelope glycoprotein GP120	-	Family
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
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
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
P [auth C], Q [auth J], R [auth Q]	PF00517	Retroviral envelope protein (GP41)	Retroviral envelope protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process 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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process regulation of leukocyte activation establishment of T cell polarity positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion establishment or maintenance of cell polarity lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of establishment of T cell polarity positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation establishment of cell polarity regulation of establishment of cell polarity immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation protein localization regulation of localization cellular localization regulation of protein localization positive regulation of receptor clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization cellular macromolecule localization macromolecule localization receptor clustering positive regulation of protein localization regulation of receptor clustering regulation of protein localization to membrane 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 symbiont-mediated perturbation of host defense response response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus modulation by symbiont of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process 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 transport of virus viral gene expression viral protein processing	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane
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 plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region
E [auth B], G [auth I], I [auth P]	10-1074 Fab Light Chain	-	-	-
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 plasma membrane membrane cellular anatomical entity protein-containing complex immunoglobulin complex extracellular region
K [auth N], M [auth E], O [auth L]	1-55 Fab Light Chain	-	-	extracellular region cellular anatomical entity
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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process 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 establishment of T cell polarity regulation of establishment or maintenance of cell polarity multicellular organismal process establishment of lymphocyte polarity regulation of cellular process regulation of leukocyte activation establishment of T cell polarity positive regulation of biological process regulation of cell activation positive regulation of leukocyte cell-cell adhesion establishment or maintenance of cell polarity lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell adhesion cell-cell adhesion T cell activation positive regulation of establishment of T cell polarity positive regulation of leukocyte activation regulation of multicellular organismal process regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of cellular process regulation of biological process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation biological regulation regulation of T cell activation establishment of cell polarity regulation of establishment of cell polarity immune system process regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation protein localization regulation of localization cellular localization regulation of protein localization positive regulation of receptor clustering positive regulation of protein localization to membrane localization within membrane protein localization to membrane localization regulation of cellular localization cellular macromolecule localization macromolecule localization receptor clustering positive regulation of protein localization regulation of receptor clustering regulation of protein localization to membrane 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 symbiont-mediated perturbation of host defense response response to host defenses response to stimulus response to other organism response to defenses of other organism modulation by virus of host process response to external stimulus virus-mediated perturbation of host defense response response to biotic stimulus modulation by symbiont of host process response to host response to external biotic stimulus modulation of process of another organism modulation by virus of host cellular process 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 transport of virus viral gene expression viral protein processing	virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region virion component virion membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane cellular anatomical entity host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cell periphery plasma membrane membrane viral membrane viral envelope host cell plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
D [auth A], F, H [auth O]	IPR003597	Immunoglobulin C1-set	Domain
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]	IPR003599	Immunoglobulin subtype	Domain
D [auth A], F, H [auth O]	IPR013106	Immunoglobulin V-set domain	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
E [auth B], G [auth I], I [auth P]	IPR003597	Immunoglobulin C1-set	Domain
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]	IPR003599	Immunoglobulin subtype	Domain
E [auth B], G [auth I], I [auth P]	IPR013106	Immunoglobulin V-set domain	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
J [auth M], L [auth D], N [auth H]	IPR003597	Immunoglobulin C1-set	Domain
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]	IPR003599	Immunoglobulin subtype	Domain
J [auth M], L [auth D], N [auth H]	IPR013106	Immunoglobulin V-set domain	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
K [auth N], M [auth E], O [auth L]	IPR003597	Immunoglobulin C1-set	Domain
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]	IPR003599	Immunoglobulin subtype	Domain
K [auth N], M [auth E], O [auth L]	IPR013106	Immunoglobulin V-set domain	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
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